Re: [Rd] FR: Customize background colour of row and column headers for the View output

2024-05-16 Thread Ivan Krylov via R-devel
The change suggested by Iago Giné Vázquez is indeed very simple. It sets the background colour of the row and column headers to the background of the rest of the dataentry window. With this patch, R passes 'make check'. As Duncan Murdoch mentions, the X11 editor already behaves this way. If it's

Re: [Rd] [External] R hang/bug with circular references and promises

2024-05-13 Thread Ivan Krylov via R-devel
On Mon, 13 May 2024 09:54:27 -0500 (CDT) luke-tierney--- via R-devel wrote: > Looks like I added that warning 22 years ago, so that should be enough > notice :-). I'll look into removing it now. Dear Luke, I've got a somewhat niche use case: as a way of protecting myself against rogue *.rds

Re: [Rd] max on numeric_version with long components

2024-04-27 Thread Ivan Krylov via R-devel
В Sat, 27 Apr 2024 13:56:58 -0500 Jonathan Keane пишет: > In devel: > > max(numeric_version(c("1.0.1.1", "1.0.3.1", > "1.0.2.1"))) > [1] ‘1.0.1.1’ > > max(numeric_version(c("1.0.1.1000", "1.0.3.1000", > "1.0.2.1000"))) > [1] ‘1.0.3.1000’ Thank

Re: [Rd] R 4.4.0 has version of Matrix 1.7-0, but it's not available on CRAN

2024-04-26 Thread Ivan Krylov via R-devel
On Fri, 26 Apr 2024 13:15:47 +0200 Gábor Csárdi wrote: > That's not how this worked in the past AFAIR. Simply, the packages in > the x.y.z/Recommended directories were included in > src/contrib/PACKAGES*, metadata, with the correct R version > dependencies, in the correct order, so that

Re: [Rd] R 4.4.0 has version of Matrix 1.7-0, but it's not available on CRAN

2024-04-26 Thread Ivan Krylov via R-devel
On Fri, 26 Apr 2024 12:32:59 +0200 Martin Maechler wrote: > Finally, I'd think it definitely would be nice for > install.packages("Matrix") to automatically get the correct > Matrix version from CRAN ... so we (R-core) would be grateful > for a patch to install.packages() to achieve this Since

Re: [Rd] Big speedup in install.packages() by re-using connections

2024-04-25 Thread Ivan Krylov via R-devel
On Thu, 25 Apr 2024 14:45:04 +0200 Jeroen Ooms wrote: > Thoughts? How verboten would it be to create an empty external pointer object, add it to the preserved list, and set an on-exit finalizer to clean up the curl multi-handle? As far as I can tell, the internet module is not supposed to be

Re: [Rd] [External] Re: Is ALTREP "non-API"?

2024-04-25 Thread Ivan Krylov via R-devel
On Wed, 24 Apr 2024 15:31:39 -0500 (CDT) luke-tierney--- via R-devel wrote: > We would be better off (in my view, not necessarily shared by others > in R-core) if we could get to a point where: > > all entry points listed in installed header files can be used in > packages, at least

Re: [Rd] View() segfaulting ...

2024-04-25 Thread Ivan Krylov via R-devel
On Wed, 24 Apr 2024 19:35:42 -0400 Ben Bolker wrote: > I'm using bleeding-edge R-devel, so maybe my build is weird. Can > anyone else reproduce this? > >View() seems to crash on just about anything. Not for me, sorry. If you have a sufficiently new processor, you can use `rr` [*] to

Re: [Rd] Wish: a way to track progress of parallel operations

2024-04-09 Thread Ivan Krylov via R-devel
Dear Henrik (and everyone else): Here's a patch implementing support for immediateConditions in 'parallel' socket clusters. What do you think? I've tried to make the feature backwards-compatible in the sense that an older R starting a newer cluster worker will not pass the flag enabling

Re: [Rd] Bug in out-of-bounds assignment of list object to expression() vector

2024-04-05 Thread Ivan Krylov via R-devel
On Fri, 5 Apr 2024 08:15:20 -0400 June Choe wrote: > When assigning a list to an out of bounds index (ex: the next, n+1 > index), it errors the same but now changes the values of the vector > to NULL: > > ``` > x <- expression(a,b,c) > x[[4]] <- list() # Error > x > #> expression(NULL, NULL,

Re: [Rd] hand compile; link to MKL fails at BLAS zdotu

2024-03-30 Thread Ivan Krylov via R-devel
В Sat, 30 Mar 2024 20:31:25 +0300 Ivan Krylov via R-devel пишет: > It seems to crash inside MKL! Should have read some more about mkl_gf_lp64 before posting. According to the Intel forums, it is indeed required in order to work with the GFortran calling convention, but if you're linking agai

Re: [Rd] hand compile; link to MKL fails at BLAS zdotu

2024-03-30 Thread Ivan Krylov via R-devel
В Sat, 30 Mar 2024 10:55:48 + Ramón Fallon пишет: > In contrast to Dirk's solution, I've found R's configure script > doesn't recognise the update-alternatives system on debian/ubuntu, if > it's MKL. It ought to work if configured with --with-blas=-lblas --with-lapack=-llapack, but, as you

Re: [Rd] paths capability FALSE on devel?

2024-03-27 Thread Ivan Krylov via R-devel
В Wed, 27 Mar 2024 11:28:17 +0100 Alexandre Courtiol пишет: > after installing R-devel the output of > grDevices::dev.capabilities()$paths is FALSE, while it is TRUE for R > 4.3.3 Your system must be missing Cairo development headers, making x11() fall back to type = 'Xlib': $ R-devel -q -s -e

Re: [Rd] Wish: a way to track progress of parallel operations

2024-03-26 Thread Ivan Krylov via R-devel
Henrik, Thank you for taking the time to read and reply to my message! On Mon, 25 Mar 2024 10:19:38 -0700 Henrik Bengtsson wrote: > * Target a solution that works the same regardless whether we run in > parallel or not, i.e. the code/API should look the same regardless of > using, say,

[Rd] Wish: a way to track progress of parallel operations

2024-03-25 Thread Ivan Krylov via R-devel
Hello R-devel, A function to be run inside lapply() or one of its friends is trivial to augment with side effects to show a progress bar. When the code is intended to be run on a 'parallel' cluster, it generally cannot rely on its own side effects to report progress. I've found three approaches

Re: [Rd] Spurious warning in as.data.frame.factor()

2024-03-17 Thread Ivan Krylov via R-devel
On Fri, 15 Mar 2024 11:24:22 +0100 Martin Maechler wrote: > I think just adding > > removeGeneric('as.data.frame') > > is appropriate here as it is self-explaining and should not leave > much traces. Thanks for letting me know! I'll make sure to use removeGeneric() in similar cases in

Re: [Rd] Spurious warning in as.data.frame.factor()

2024-03-14 Thread Ivan Krylov via R-devel
On Thu, 14 Mar 2024 10:41:54 +0100 Martin Maechler wrote: > Anybody trying S7 examples and see if they work w/o producing > wrong warnings? It looks like this is not applicable to S7. If I overwrite as.data.frame with a newly created S7 generic, it fails to dispatch on existing S3 classes:

Re: [Rd] Spurious warning in as.data.frame.factor()

2024-03-13 Thread Ivan Krylov via R-devel
В Tue, 12 Mar 2024 12:33:17 -0700 Hervé Pagès пишет: > The acrobatics that as.data.frame.factor() is going thru in order to > recognize a direct call don't play nice if as.data.frame() is an S4 > generic: > >     df <- as.data.frame(factor(11:12)) > >    

[Rd] Never exporting .__global__ and .__suppressForeign__?

2024-03-06 Thread Ivan Krylov via R-devel
Hello, (Dear Richard, I hope you don't mind being Cc:'d on this thread in R-devel. This is one of the ways we can prevent similar problems from happening in the future.) Sometimes, package authors who use both exportPattern('.') and utils::globalVariables(...) get confusing WARNINGs about

[Rd] How to avoid the Markdown code block bug on R Bugzilla

2024-02-27 Thread Ivan Krylov via R-devel
Hello, There's a rare but annoying bug in Bugzilla 5.1.2...5.3.2+ where a Markdown code block inside a comment may be replaced by U+F111 or U+F222, and then the following code blocks may end up being replaced by the preceding ones. For example, the problem can be seen in PR16158:

Re: [Rd] Tcl socket server (tcltk) does not work any more on R 4.3.2

2024-02-21 Thread Ivan Krylov via R-devel
В Wed, 21 Feb 2024 08:01:16 +0100 "webmail.gandi.net" пишет: > Since the {tcltk} package was working fine with "while > (Tcl_DoOneEvent(TCL_DONT_WAIT) && max_ev) max_ev—;", unless there is > a clear performance enhancement with "while (i-- && > Tcl_ServiceAll())", it would perhaps be wise to

Re: [Rd] Tcl socket server (tcltk) does not work any more on R 4.3.2

2024-02-20 Thread Ivan Krylov via R-devel
В Tue, 20 Feb 2024 12:27:35 +0100 "webmail.gandi.net" пишет: > When R process #1 is R 4.2.3, it works as expected (whatever version > of R #2). When R process #1 is R 4.3.2, nothing is sent or received > through the socket apparently, but no error is issued and process #2 > seems to be able to

Re: [Rd] certain pipe() use cases not working in r-devel

2024-02-15 Thread Ivan Krylov via R-devel
В Wed, 14 Feb 2024 14:43:12 -0800 Jennifer Bryan пишет: > But in r-devel on macOS, this is silent no-op, i.e. "hello, world" > does not print: > > > R.version.string > [1] "R Under development (unstable) (2024-02-13 r85895)" > > con <- pipe("cat") > > writeLines("hello, world", con) I can

Re: [Rd] Difficult debug

2024-02-07 Thread Ivan Krylov via R-devel
On Wed, 07 Feb 2024 14:01:44 -0600 "Therneau, Terry M., Ph.D. via R-devel" wrote: > > test2 <- mysurv(fit2, pbc2$bili4, p0= 4:0/10, fit2, x0 =50) > ==31730== Invalid read of size 8 > ==31730==    at 0x298A07: Rf_allocVector3 (memory.c:2861) > ==31730==    by 0x299B2C: Rf_allocVector

Re: [Rd] Advice debugging M1Mac check errors

2024-02-05 Thread Ivan Krylov via R-devel
On Sun, 4 Feb 2024 20:41:51 +0100 Holger Hoefling wrote: > I wanted to ask if people have good advice on how to debug M1Mac > package check errors when you don´t have a Mac? Apologies for not answering the question you asked, but is this about hdf5r and problems printing R_xlen_t [*] that

Re: [Rd] [External] Re: Choices to remove `srcref` (and its buddies) when serializing objects

2024-01-18 Thread Ivan Krylov via R-devel
On Thu, 18 Jan 2024 09:59:31 -0600 (CST) luke-tier...@uiowa.edu wrote: > What does 'blow up' mean? If it is anything other than signal a "bad > binding access" error then it would be good to have more details. My apologies for not being precise enough. I meant the "bad binding access" error in

Re: [Rd] Choices to remove `srcref` (and its buddies) when serializing objects

2024-01-18 Thread Ivan Krylov via R-devel
В Tue, 16 Jan 2024 14:16:19 -0500 Dipterix Wang пишет: > Could you recommend any packages/functions that compute hash such > that the source references and sexpinfo_struct are ignored? Basically > a version of `serialize` that convert R objects to raw without > storing the ancillary source

Re: [Rd] Sys.which() caching path to `which`

2024-01-12 Thread Ivan Krylov via R-devel
On Thu, 11 Jan 2024 09:30:55 +1300 Simon Urbanek wrote: > That said, WHICH is a mess - it may make sense to switch to the > command -v built-in which is part of POSIX (where available - which > is almost everywhere today) which would not require an external tool This is a bit tricky to

Re: [Rd] Choices to remove `srcref` (and its buddies) when serializing objects

2024-01-12 Thread Ivan Krylov via R-devel
В Fri, 12 Jan 2024 00:11:45 -0500 Dipterix Wang пишет: > I wonder how hard it would be to have options to discard source when > serializing R objects? > Currently my analyses heavily depend on digest function to generate > file caches and automatically schedule pipelines (to update cache) >

Re: [Rd] using Paraview "in-situ" with R?

2024-01-09 Thread Ivan Krylov via R-devel
В Tue, 9 Jan 2024 14:20:17 + Mike Marchywka пишет: > it seems like an excellent tool to interface to R allowing > visualization without a bunch of temp files or > > Is anyone aware of anyone doing this interface or reasons its a > boondoggle? This sounds like it's better suited for