[Rd] Sys.timezone (timedatectl) unnecessarily warns loudly

n = TRUE) +inf <- suppressWarnings(system("timedatectl", intern = TRUE, ignore.stderr=TRUE)) ## typical format: ## " Time zone: Europe/London (GMT, +)" ## " Time zone: Europe/Vienna (CET, +0100)" Regards, Jan Gorecki

[Rd] base::mean not consistent about NA/NaN

Hi, base::mean is not consistent in terms of handling NA/NaN. Mean should not depend on order of its arguments while currently it is. mean(c(NA, NaN)) #[1] NA mean(c(NaN, NA)) #[1] NaN I created issue so in case of no replies here status of it can be looked up at: https://bugs.r-p

Re: [Rd] base::mean not consistent about NA/NaN

> > > > On Mon, Jul 2, 2018 at 5:32 PM, Duncan Murdoch > wrote: > > On 02/07/2018 11:25 AM, Jan Gorecki wrote: > >> Hi, > >> base::mean is not consistent in terms of handling NA/NaN. > >> Mean should not depend on order of its arguments while curren

Re: [Rd] base::mean not consistent about NA/NaN

t commutative: >> >> > NA + NaN >> [1] NA >> > NaN + NA >> [1] NaN >> >> >> >> On Mon, Jul 2, 2018 at 5:32 PM, Duncan Murdoch >> wrote: >>> On 02/07/2018 11:25 AM, Jan Gorecki wrote: >>>> Hi, >>>&g

Re: [Rd] Runnable R packages

eployment. For those processes you might find tools4pkgs branch in base R useful (packages.dcf, mirror.packages functions), unfortunately not merged: https://github.com/wch/r-source/compare/tools4pkgs Jan Gorecki On Thu, Jan 31, 2019 at 9:08 PM Barry Rowlingson wrote: > > On Thu, Jan 31, 2019 at 3

Re: [Rd] nrow(rbind(character(), character())) returns 2 (as documented but very unintuitive, IMHO)

issues/2422 You should find that discussion useful. Best, Jan Gorecki On Fri, May 17, 2019 at 8:11 AM Pages, Herve wrote: > > On 5/16/19 17:48, Gabriel Becker wrote: > > Hi Herve, > > Inline. > > > > On Thu, May 16, 2019 at 4:45 PM Pages, Herve > mailto:hpa...@f

Re: [Rd] R pkg install should fail for unsuccessful DLL copy on windows?

Hi Toby, AFAIK it has not been addressed in R. You can handle the problem on your package side, see https://github.com/Rdatatable/data.table/pull/3237 Regards, Jan On Thu, May 30, 2019 at 4:46 AM Toby Hocking wrote: > > Hi all, > > I am having an issue related to installing packages on windows w

Re: [Rd] Underscores in package names

gains. There is nothing wrong in having package "a.pkg" and function "a_pkg()". Regards, Jan Gorecki On Fri, Aug 16, 2019 at 1:20 AM Abby Spurdle wrote: > > > While > > package names are not functions, using dots in package names > > encourages the use o

[Rd] REprintf could be caught by tryCatch(message)

can catch it? So in the example below catch(Cmessage()) would behave consistently to R's catch(message("a"))? Regards, Jan Gorecki catch = function(expr) { tryCatch(expr, message=function(m) cat("caught message\n"), warning=function(w) cat("caught warning\

Re: [Rd] [External] REprintf could be caught by tryCatch(message)

ey, Luke wrote: > > On Sun, 15 Sep 2019, Jan Gorecki wrote: > > > Dear R-devel community, > > > > There appears to be an inconsistency in R C API about the exceptions > > that can be raised from C code. > > Mapping of R C funs to corresponding R functio

Re: [Rd] [External] REprintf could be caught by tryCatch(message)

h I doubt > it will rise to the top of anyone's priority list. > > Best, > > luke > > On Sun, 15 Sep 2019, Jan Gorecki wrote: > > > Thank you Luke for prompt reply. > > Is it possible then to request a new function to R C API "message" > >

Re: [Rd] passing extra arguments to devtools::build

Dear Michael, I think R-devel mailing list is not a proper place to report issues with devtools. I would try filling an issue in their github repository. If you are able to reproduce this issue using plain R without any extra packages, then please provide such example here. Regards, Jan Gorecki

[Rd] speed up R_IsNA, R_IsNaN for vector input

a.out R_IsNaN 8 ./a.out ISNAN 8 Best regards, Jan Gorecki __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] speed up R_IsNA, R_IsNaN for vector input

30, 2019 at 10:31 AM Tomas Kalibera wrote: > > On 9/29/19 1:09 PM, Jan Gorecki wrote: > > Dear R developers, > > > > I spotted that R_isNA and R_IsNaN could be improved when applied on a > > vector where we could take out small part of their logic, run it once, >

[Rd] contrib.url and R-devel numbering 3.7 vs 4.0

stion from May 2018 that makes contrib.url more flexible, allowing to handle issue discussed in this email. https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17420 Best Regards, Jan Gorecki __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

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

Gabriel, My view is rather radical. - head/tail should return object having same number of dimensions - data.frame should be a special case - matrix should be handled as 2D array P.S. idea of accepting `n` argument as a vector of corresponding dimensions is a brilliant one On Wed, Oct 30, 2019 a

[Rd] R C api for 'inherits' S3 and S4 objects

allocation, thread safe). This is unfortunately not possible for S4 classes. I would kindly request new function in R C api so it can be achieved for S4 classes with no risk of allocation. For reference mentioned functions below. Thank you. Jan Gorecki // S3 inheritance bool INHERITS(SEXP x, SEXP char_

Re: [Rd] [External] R C api for 'inherits' S3 and S4 objects

Thank you Luke. That is why I don't use Rf_inherits but INHERITS which does not allocate, provided in the email body. I cannot do similarly for S4 classes, thus asking for some API for that. On Fri, Nov 1, 2019 at 5:56 PM Tierney, Luke wrote: > > On Fri, 1 Nov 2019, Jan Gorecki wrote:

Re: [Rd] [External] R C api for 'inherits' S3 and S4 objects

Thank you all for your valuable comments. Best, Jan On Fri, Nov 1, 2019 at 8:15 PM Tierney, Luke wrote: > > On Fri, 1 Nov 2019, Jan Gorecki wrote: > > > Thank you Luke. > > That is why I don't use Rf_inherits but INHERITS which does not > > allocate, prov

Re: [Rd] class() |--> c("matrix", "arrary") -- and S3 dispatch

In case if anyone needs daily R-devel there is my build scheduled on GitLab. As of now based on Ubuntu 16.04, R built using: --with-recommended-packages --enable-strict-barrier --disable-long-double Predefined Makevars for building pkgs using: -g -O2 -Wall -pedantic -fstack-protector-strong -D_FORT

[Rd] data.frame could handle long vectors

Dear R-devel, It seems that data.frame class could be improved to handle long vectors better. It fails while using `data.frame(.)` and the same using, I believe, lower overhead, `as.data.frame(list(.)). Please find reproducible example below, tested on 2019-12-01 r77492. id1 = sample.int(3e9, rep

[Rd] head/tail breaking change

] [,2] [,3] #[3,] 21 24 27 Best, Jan Gorecki __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] head/tail breaking change

es and for matrices, which are now > explicitly array objects with 2 dimensions as well as classed as matrices, > so its more consistent now, and more reasonable for the object). > > Best, > ~G > > On Wed, Dec 18, 2019 at 2:44 AM Jan Gorecki wrote: > >> Hi R-deve

[Rd] New R function is.nana = is.na & !is.nan

mitive("is.nana") else .Primitive("is.na") Then probably a copy of C function `do_isnan` as `do_isnana` with a minor change from `R_IsNaN` to `R_IsNA`. Best, Jan Gorecki __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] New R function is.nana = is.na & !is.nan

e to add an extra argument (e.g. 'strict') to > is.na(). FALSE by default, and ignored (with or w/o a warning) when the > type of 'x' is not "numeric". > > H. > > > On 12/31/19 22:16, Jan Gorecki wrote: > > Hello R-devel, > > > >

Re: [Rd] A bug understanding F relative to FALSE?

I agree it is not good to have those symbols used in packages, but I found to use those quite often in my developement workflow, which is something like: $ R -q > cc(F) where `cc` is my function to rebuild application to recent state. I use it really often. Having to type FALSE every time

[Rd] document base::`[[.data.frame`

internally, then maybe better to put that into own internal function? Best regards, Jan Gorecki __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

[Rd] new bquote feature splice does not address a common LISP @ use case?

..(b), splice=TRUE) d #6 - (5 + 4) There is corresponding LISP code provided CL-USER> (setf b `(5 + 4)) (5 + 4) CL-USER> (setf c `(6 - ,@b)) (6 - 5 + 4) CL-USER> (setf c-non-spliced `(6 - ,b)) (6 - (5 + 4)) CL-USER> Thanks, Jan Gorecki __ R

Re: [Rd] new bquote feature splice does not address a common LISP @ use case?

Thank you Lionel for comprehensive explanation. I think that rotating AST in base R is not a good way to go, it would probably complicate the code heavily. Best, Jan Gorecki On Tue, Mar 17, 2020 at 4:49 PM Lionel Henry wrote: > > Hi Jan, > > In the lisp code you provide the operator

[Rd] substitute inconsistent output

(1L,2L))) #v + 1:2 substitute(v+x, list(x=c(0L,2L))) #v + c(0L, 2L) Thank you, Jan Gorecki __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

[Rd] is.vector could handle AsIs class better

there any reason behind this behaviour? Could we have it supported so AsIs class is ignored when `is.vector` is doing its job? Best Regards, Jan Gorecki __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] is.vector could handle AsIs class better

er > the documentation. In this case its class of "AsIs". > > Best, > ~G > > On Sun, Mar 29, 2020 at 6:29 AM Jan Gorecki wrote: >> >> Dear R-devel, >> >> AsIs class seems to be well handled by `typeof` and `mode` function. >> Those two

Re: [Rd] Add a new environment variable switch for the 'large version' check

For the same reason, handling false positive in CRAN checks, there are other places that could be improved. Like "size of tarball" NOTE. If one could control this size with an environment variable. Similarly to the proposal made by Jim. It would be useful as well. On Thu, Apr 16, 2020 at 5:06 PM H

Re: [Rd] Demo for linking native routines between R packages

have a "hello world from C" package linked from WRE. All those native routines registration, the proper way, is not really that obvious. It would be much easier to learn from a package that doesn't have any other logic. Best wishes, Jan Gorecki On Fri, Apr 17, 2020 at 3:32 PM Zhang, Ji

Re: [Rd] mclapply returns NULLs on MacOS when running GAM

> PS. Simon, I think your explicit comment on mcparallel() & friends is very helpful for many people and developers. It clearly tells developers to never use mclapply() as the only path through their code. I'm quite sure not everyone has been or is aware of this. Now it's clear. Thank you. I secon

[Rd] system(timeout=) may timeout with 0 exit code

uot;' timed out(?) but still exited with 0 code, timeout 7200s, took 7220.005s, warning '/bin/bash -c "./_launcher/solution.R > log.out 2> log.err"' timed out after 7200s' Thank you, Jan Gorecki __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

[Rd] update R Internals for R 4.0.0

erseded by REFCNT. There might be of course other places that needs update, but this one is important feature of R 4.0.0. Thank you, Jan Gorecki __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

[Rd] order function called on a data.frame?

Best Regards, Jan Gorecki __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

[Rd] base::order breaking change in R-devel

,x2)) #[1] 1 4 2 3 Encoding(x2) = "unknown" base::order(c(x2,x1,x1,x2)) #[1] 2 3 1 4 # R-devel base::order(c(x2,x1,x1,x2)) #[1] 1 2 3 4 Encoding(x2) = "unknown" base::order(c(x2,x1,x1,x2)) #[1] 1 4 2 3 Best Regards, Jan Gorecki __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

[Rd] Running package tests and not stop on first fail

after first fail. Do you think it could be optionally available to continue to run tests after failures? Regards, Jan Gorecki [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Running package tests and not stop on first fail

. Regards, Jan On 3 November 2016 at 17:25, Hervé Pagès wrote: > > Hi Martin, Jan, > > On 11/03/2016 03:45 AM, Martin Maechler wrote: >>>>>>> >>>>>>> Jan Gorecki >>>>>>> on Tue, 1 Nov 2016 22:51:28 + writes: >> &

Re: [Rd] Running package tests and not stop on first fail

Sorry for late reply. I like the stop-on-error. Thanks for merging. Glad to be R contributor! On 4 November 2016 at 09:42, Oliver Keyes wrote: > On Friday, 4 November 2016, Martin Maechler > wrote: >> >> > Dirk Eddelbuettel >> > on Fri, 4 Nov 2016 10:36:52 -0500 writes: >> >> >

Re: [Rd] new function to tools/utils package: dependencies based on DESCRIPTION file

ed together with R. They doesn't require any OS dependencies >>> or R dependencies, unlike devtools which requires both. Installing >>> unnecessary OS dependencies and R dependencies just for such a simple >>> wrapper doesn't seem to be an elegant way to ad

[Rd] colnames for data.frame could be greatly improved

Hello, colnames seems to be not optimized well for data.frame. It escapes processing for data.frame in if (is.data.frame(x) && do.NULL) return(names(x)) but only when do.NULL true. This makes huge difference when do.NULL false. Minimal edit to `colnames`: if (is.data.frame(x)) {

Re: [Rd] colnames for data.frame could be greatly improved

Hi there, Any update on this? Should I create bugzilla ticket and submit patch? Regards Jan Gorecki On 20 December 2016 at 01:27, Jan Gorecki wrote: > Hello, > > colnames seems to be not optimized well for data.frame. It escapes > processing for data.frame in > > i

Re: [Rd] order function called on a data.frame?

2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 > > > #[43] 17 18 19 20 21 22 23 24 25 26 > > > > > > > > > And I agree that order with data.frames should give a warning. The > > > result is indeed useless: > > > > > > data.frame(letters,

[Rd] fixed url for R-release windows binaries

Dear R-developers, Could we have a fixed url to fetch current R-release windows binaries? Like we do for R-devel https://cloud.r-project.org/bin/windows/base/R-devel-win.exe Something like the following would do https://cloud.r-project.org/bin/windows/base/R-release-win.exe Thank you, Jan

[Rd] R-devel internal errors during check produce?

reproduce download current data.table from CRAN (1.12.8) and run R check Best regards, Jan Gorecki __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] R-devel internal errors during check produce?

recki/dockerfiles/-/raw/master/r-devel/Dockerfile On Sat, Jun 27, 2020 at 12:37 AM Jan Gorecki wrote: > > Hi R developers, > > On R-devel (2020-06-24 r78746) I am getting those two new exceptions > during R check. I found a change which eventually may be related > https://github.

Re: [Rd] R-devel internal errors during check produce?

quot;package:stats"), as.environment("package:utils"), as.environment("package:methods") ) unique(env_list) Best regards, Jan On Mon, Jun 29, 2020 at 5:42 PM Martin Maechler wrote: > > >>>>> Kurt Hornik > >>>>> on Mon

Re: [Rd] R-devel internal errors during check produce?

: > > >>>>> Kurt Hornik > >>>>> on Tue, 30 Jun 2020 06:20:57 +0200 writes: > > >>>>> Jan Gorecki writes: > >> Thank you both, You are absolutely correct that example > >> should be minimal, so here it is. > > >&g

Re: [Rd] Build a R call at C level

It is quite known that R documentation on R C api could be improved... Still R-package-devel mailing list should be preferred for this kind of questions. Not sure if that is the best way, but works. call_to_sum <- inline::cfunction( language = "C", sig = c(x = "SEXP"), body = " SEXP e = PROTE

[Rd] .Internal(quit(...)): system call failed: Cannot allocate memory

before it raises this warning? Best regards, Jan Gorecki __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] .Internal(quit(...)): system call failed: Cannot allocate memory

all=, op=, > args=0x57813f90, rho=) at main.c:1393 > > -Bill > > On Mon, Nov 23, 2020 at 3:15 AM Tomas Kalibera > wrote: >> >> On 11/21/20 6:51 PM, Jan Gorecki wrote: >> > Dear R-developers, >> > >> > Some of the more fat scripts (50+ GB mem

Re: [Rd] .Internal(quit(...)): system call failed: Cannot allocate memory

ocess took, how many objects it has to check on each level. Best regards, Jan On Tue, Nov 24, 2020 at 1:05 PM Tomas Kalibera wrote: > > On 11/24/20 11:27 AM, Jan Gorecki wrote: > > Thanks Bill for checking that. > > It was my impression that warnings are raised from some in

Re: [Rd] [External] Re: .Internal(quit(...)): system call failed: Cannot allocate memory

Thank you Luke for looking into it. Your knowledge of gc is definitely helpful here. I put comments inline below. Best, Jan On Wed, Nov 25, 2020 at 10:38 PM wrote: > > On Tue, 24 Nov 2020, Jan Gorecki wrote: > > > As for other calls to system. I avoid calling system. In the past

Re: [Rd] [External] Re: .Internal(quit(...)): system call failed: Cannot allocate memory

es: 391149 Involuntary context switches: 646410 File system inputs: 106605648 File system outputs: 120 On Fri, Nov 27, 2020 at 10:18 PM wrote: > > On Thu, 26 Nov 2020, Jan Gorecki wrote: > > > Thank you Luke for looking into it. Your knowledge of gc is definitel

Re: [Rd] [External] Re: .Internal(quit(...)): system call failed: Cannot allocate memory

Gb /usr/bin/time bin/Rscript jg.R 1e9 2e0 0 0 > > (your code in jg.R). I get a quick failure with 11785524maxresident)k > > Best, > > luke > > On Tue, 1 Dec 2020, Jan Gorecki wrote: > > > Thank you Luke, > > > > I tried your suggestion about R_MAX_VSIZE bu

Re: [Rd] [External] Re: New pipe operator

Luke, When writing a blog post on that, could you please describe performance implications that this new feature will carry? AFAIU, compared to a standard way of using temporary variables, pipes will allow to not increment REFCNT of objects being piped into. Therefore peak memory usage could be low

[Rd] as.POSIXct.numeric change default of origin argument

having that as a default seems reasonable. Proposed change seems to be pretty safe because it is now an error. Best Regards, Jan Gorecki __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] In function isum in summary.c, k should be R_xlen_t

Don't know this piece well but I am guessing that you haven't found an example because the iterator is going up to the length of a vector anymore but only to the number of batches, which is unlikely to be more than 2^31. On Tue, Dec 22, 2020 at 12:30 PM Suharto Anggono Suharto Anggono via R-devel

[Rd] R-devel new warning: no longer be an S4 object

Hi R-devs, R 4.0.5 gives no warning. Is it expected? Searching the news for "I(" doesn't give any info. Thanks z = I(getClass("MethodDefinition")) Warning message: In `class<-`(x, unique.default(c("AsIs", oldClass(x : Setting class(x) to multiple strings ("AsIs", "classRepresentation", ...);

[Rd] tools:: extracting pkg dependencies from DCF

ally makes it easier for organizations to glue together usage of their own R packages repos and CRAN repo in a smooth way. That could possibly help to offload CRAN from new submissions. gh mirror link for easy preview: https://github.com/wch/r-source/blob/tools4pkgs/src/library/tools/R/packages

Re: [Rd] tools:: extracting pkg dependencies from DCF

of their own R packages repos and CRAN repo in a >> smooth way. That could possibly help to offload CRAN from new submissions. >> >> gh mirror link for easy preview: >> >> https://github.com/wch/r-source/blob/tools4pkgs/src/library/tools/R/packages.R#L41

Re: [Rd] tools:: extracting pkg dependencies from DCF

(paste0("file://", tdir)) > > library(tools) > > package_dependencies("rtables", avl) > $rtables > [1] "methods""magrittr" "formatters" "stats" "htmltools" > [6] "grid" > > >

Re: [Rd] tools:: extracting pkg dependencies from DCF

es one could move that > functionality into a separate function - we all do that constantly for the > sites we manage, so it would be certainly something worthwhile. > > Cheers, > Simon > > > > On Oct 15, 2022, at 7:14 PM, Jan Gorecki wrote: > > > > Hi Gabriel, >

Re: [Rd] tools:: extracting pkg dependencies from DCF

functionality to be part of base R. Possibly they just don't need it themselves. Yet isn't this sufficient that hundreds/thousands of packages does need this functionality? Best regards, Jan On Mon, Oct 17, 2022 at 8:39 AM Jan Gorecki wrote: > > Gabriel and Simon > > I

Re: [Rd] tools:: extracting pkg dependencies from DCF

rself, as that is counter to install.packages' core design. > > Does that make sense? > > Best, > ~G > > On Fri, Oct 28, 2022 at 12:18 PM Jan Gorecki wrote: >> >> Gabriel, >> >> I am trying to design generic solution that could be applied to >&g

Re: [Rd] tools:: extracting pkg dependencies from DCF

and, far from ideal, but does work. Best, Jan On Fri, Oct 28, 2022 at 10:42 PM Gabriel Becker wrote: > > Hi Jan, > > > On Fri, Oct 28, 2022 at 1:57 PM Jan Gorecki wrote: >> >> Gabriel, >> >> It is the most basic CI use case. One wants to install only >

[Rd] tune "checking installed package size" NOTE

Hello, Recently we got _R_CHECK_CRAN_INCOMING_TARBALL_THRESHOLD_ env var to tune "Size of tarball" note during R package check. Could we get similar one for tuning "checking installed package size" note? We can then fit R CMD check more tightly to our package and track regression in installed si

Re: [Rd] tune "checking installed package size" NOTE

Oh, thank you. I only grep WRE. Yes it does work On Fri, Nov 24, 2023 at 12:20 PM Ivan Krylov wrote: > В Fri, 24 Nov 2023 12:15:06 +0100 > Jan Gorecki пишет: > > > Recently we got _R_CHECK_CRAN_INCOMING_TARBALL_THRESHOLD_ env var to > > tune "Size of tarball&qu

[Rd] capabilities() could report strict-barrier

Hi, I would like to propose for capabilities() function to include information about strict-barrier (--enable-strict-barrier flag). I can now do "grep barrier /usr/local/lib/R/etc/Makeconf" but having that in R, in platform independent way, would be useful. Best Regards, J

Re: [Rd] tools:: extracting pkg dependencies from DCF

Gorecki On Sat, Oct 29, 2022 at 6:26 PM Jan Gorecki wrote: > > Thank you Gabriel, > > Just for future readers. Below is a base R way to address this common > problem, as instructed by you (+stopifnot to suppress print). > > Rscript -e 'stopifnot(file.copy("DESCRIPT

Re: [Rd] eval(parse()) within mutate() returning same value for all rows

Unless you are able to reproduce the problem without dplyr then you should submit your question to dplyr issues tracker. R-devel is for issues in R, not in a third party packages. On Fri, Dec 29, 2023, 15:13 Mateo Obregón wrote: > Hi all- > > Looking through stackoverflow for R string combining