Re: [Rd] r-base: FTBFS: Add "${boot_path}/zero" for OpenJDK zero build

2025-04-17 Thread Simon Urbanek
Dandan, thanks! Dirk reported it as https://bugs.r-project.org/show_bug.cgi?id=18884 and it should be fixed in R-devel r88154 - please confirm if it works for you and if it does, I'll port it to R 4.5.0 Patched. Cheers, Simon > On Apr 17, 2025, at 3:40 PM, zhangdandan wrote: >

Re: [Rd] R CMD check and CRAN's Rust policy

2025-03-02 Thread Simon Urbanek
uages. > Why not? They all require compilers, ways to deal with dependencies and produce binaries - so does Rust. It's just one of many similar languages. The key is to have proper support instead of having each package deal with the complexities alone. Cheers, Simon __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] R CMD check and CRAN's Rust policy

2025-03-01 Thread Simon Urbanek
ndency sources etc.) are to be addressed, as opposed to making random demands. All this has nothing to do with CRAN so the issue you mention seems irrelevant to the progress. Also I'd like to know what are the "challenges embedded in R itself". Cheers, Simon > On Mar 2, 2

Re: [Rd] binary R packages for GNU/Linux

2025-02-10 Thread Simon Urbanek
it can use the CRAN binaries), so it requires cooperation across the spectrum including the distros. That said, the Linux maintainers are certainly invited to liaise with CRAN if they think it would be beneficial to host things on CRAN - we have done in the past, but with the explosion of dist

Re: [Rd] binary R packages for GNU/Linux

2025-02-10 Thread Simon Urbanek
toolchain and all library versions as well. Cheers, Simon > On Feb 10, 2025, at 10:08 PM, Tobias Verbeke > wrote: > > L.S. > > AFAICS the Writing R Extensions and R Installation and Administration manuals > do not explicitly discuss binary R packages on GNU/Linux. Only inst

Re: [Rd] 64bit integers

2025-01-25 Thread Simon Urbanek
(and breaking things) would have any benefit. Typically, the only use-case for full 64-bit integers is as opaque 64-bit storage (e.g., randomly generated IDs) but there arithmetics make no sense there and packages are already covering that need. Cheers, Simon > On Jan 25, 2025, at 11:08 PM, Ton

Re: [Rd] Will the R Project be a Mentoring Organization for GSOC 2025?

2025-01-21 Thread Simon Urbanek
Please see the GSoC schedule - for 2025 the organisation applications won't close until February 12 so we may not know the answer until possibly sometime in March (that's assuming there are proposed projects). Cheers, Simon > On Jan 22, 2025, at 6:23 AM, Greg Forkutza wrote:

Re: [Rd] Package compression benchmarks for zstd vs gzip

2025-01-15 Thread Simon Urbanek
Heather, thanks, now fixed (datasets was using numeric value for compress= instead of the compression name so it picked zstd instead of gzip - now the switch order is kept the same). Cheers, Simon > On Jan 15, 2025, at 10:21 PM, Heather Turner wrote: > > With the changes to

Re: [Rd] Package compression benchmarks for zstd vs gzip

2025-01-12 Thread Simon Urbanek
. I was thinking of using xz as that is more stable, already supported and less controversial, but I don’t think the choice really matters - it just has to be a compression which R supports (zstd and xz have different benefits, so it’s always a trade-off without a clear winner). Cheers, Simon

Re: [Rd] binomial()$linkinv no longer accepts integer values

2025-01-08 Thread Simon Urbanek
oerce integers to doubles. Technically the latter would be more consistent with R, but if someone explicitly passes an integer to the inverse logit function in a real application then chances are it’s not intentional. Cheers, Simon > Fixed in R-devel, > > Best, > Tomas > >

Re: [Rd] R_CheckUserInterrupt() can be a performance bottleneck within GUIs

2024-12-17 Thread Simon Urbanek
27;ll find code like if (++i % 1 == 0) R_CheckUserInterrupt(); in loops to make sure it's not called unnecessarily. Cheers, Simon > On Dec 18, 2024, at 4:04 AM, Ben Bolker wrote: > > This seems like a great idea. Would it help to escalate this to a post on > R-bugzilla

Re: [Rd] Is it advisable/possible to default on Linux to an EDITOR that actually exists?

2024-12-10 Thread Simon Urbanek
VISUAL - it's just a default when neither the system nor user doesn't declare their preference. I don't think R should be fishing for random programs that may or may not be editors at run-time. Cheers, Simon > On Dec 11, 2024, at 5:08 AM, Michael Chirico > wrote: > >

Re: [Rd] Exposing native httpd server

2024-12-08 Thread Simon Urbanek
Jirko, > On Dec 9, 2024, at 8:57 AM, Jiří Moravec wrote: > > Dear Simon and Jeroen, > > thank you for your answers. I have to reiterate that I am out of my depth in > here. My knowledge of http is clicking links and not much beyond that. > > I will definitely

Re: [Rd] Exposing native httpd server

2024-12-05 Thread Simon Urbanek
nt to use it for. There may be use-cases which do fit the design so we could make it happen. I would recommend looking at Rserve first, because anything implemented there is trivial to add to R (as it is the same code base) if it would make sense. So I'm open to suggestions, but they

Re: [Rd] Embedding R in other applications as a scripting language

2024-10-13 Thread Simon Urbanek
to use C++ then RInside is a nice package that wraps the R API in C++ classes for easier use: https://github.com/eddelbuettel/rinside simplifying it quite a bit. Cheers, Simon PS: this list is for the discussions on *development* of R itself, please consider using the R-help mailing list

Re: [Rd] Can gzfile be given the same method option as file

2024-09-12 Thread Simon Andrews via R-devel
В Thu, 12 Sep 2024 15:06:50 + Simon Andrews пишет: > > > download.file('https://seurat.nygenome.org/azimuth/references/homolo > > > gs.rds', destfile = "c:/Users/andrewss/homologs.rds", method="curl") <...> > > cu

Re: [Rd] Can gzfile be given the same method option as file

2024-09-12 Thread Simon Andrews via R-devel
tion was unable to check revocation for the certificate. Error in download.file("https://seurat.nygenome.org/azimuth/references/homologs.rds";, : 'curl' call had nonzero exit status I realise that this may not be as simple as the certificate not being seen, and that t

[Rd] Can gzfile be given the same method option as file

2024-09-12 Thread Simon Andrews via R-devel
onnection(g, open = "r") : the 'wininet' method of url() is deprecated for http:// and https:// URLs So I get a warning, but it works. I guess this boils down to two questions: 1. Is it possible to add the same "method" argument to gzfi

Re: [Rd] Large vector support in data.frames

2024-07-03 Thread Simon Urbanek
data frames for large data which removes the limit and allows parallel processing - but requires support from the methods that will be applied to them). Cheers, Simon > On Jul 2, 2024, at 16:04, Ivan Krylov via R-devel > wrote: > > В Wed, 19 Jun 2024 09:52:20 +0200 > Jan van

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

2024-04-26 Thread Simon Urbanek
t and some may take longer than others to settle. Feel free to report, but please don't speculate or try to "help". That said, you may find that this thread is obsolete by now (thanks to Kurt!), so no need to respond. Cheers, Simon > On Apr 26, 2024, at 11:15 PM, Gábor Csárdi

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

2024-04-24 Thread Simon Urbanek
elevant text from R-exts which is the canonical source of information. If you have issues, find some parts unclear and want to improve the documentation, I would like to invite you to contribute constructively, propose changes, submit patches. The R-exts document has been around for decades, so it seem implausible that all of sudden it is being misunderstood the way you portrayed it, but it is certainly a good idea to improve documentation so contributions are welcome. Cheers, Simon __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

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

2024-04-23 Thread Simon Urbanek
nstalled header file. These can be used in distributed packages and will only be changed after deprecation. It says "in this manual" - I don't see anywhere restriction on a particular section of the manual, so I really don't see why you would think that allocation is

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

2024-04-22 Thread Simon Urbanek
> On Apr 23, 2024, at 10:29 AM, Hadley Wickham wrote: > > > > On Mon, Apr 22, 2024 at 5:14 PM Simon Urbanek > wrote: > > > > On Apr 22, 2024, at 7:37 PM, Gabriel Becker wrote: > > > > Hi Yutani, > > > > ALTREP is part of the off

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

2024-04-22 Thread Simon Urbanek
and is not part of the API, but the development and stability of the API in some sense should get better as more packages are using it. Therefore it is currently allowed on CRAN in the hope that it will transition to stable at some point, but package authors using it must be willing to ada

Re: [Rd] RSS Feed of NEWS needs a hand

2024-04-02 Thread Simon Urbanek
Duncan, I have fixed up the repo with git restore-mtime -- I think that should solve it - please check if it did what we needed. Cheers, Simon > On Apr 3, 2024, at 2:41 AM, Duncan Murdoch wrote: > > On 02/04/2024 8:50 a.m., Dirk Eddelbuettel wrote: >> On 2 April 2024

Re: [Rd] Advice debugging M1Mac check errors

2024-02-06 Thread Simon Urbanek
e on where in > our manual to look this up. > > The mac-builder service offers checks for R 4.3.0, the 'development' option > being (last time I tried) the same as the 'release' option. (When I asked, > Simon said that 'development' checks were only

Re: [Rd] Advice debugging M1Mac check errors

2024-02-04 Thread Simon Urbanek
once Microsoft's glacial move is done we'll be likely seeing only 64-bit everywhere. That said even if you don't have a arm64 CPU, you can build R with --disable-long-double to get closer to the arm64 results if that is your worry. Cheers, Simon > > On 04/02/2024 4:47 p.m

Re: [Rd] [Feature Request] Hide API Key in download.file() / R's libcurl

2024-02-03 Thread Simon Urbanek
ke to see under what conditions - and how you think that will solve the problem. Cheers, Simon > On Feb 2, 2024, at 5:28 AM, Xinyi wrote: > > Hi all, > > When trying to install a package from R using install.packages(), it will > print out the full url address (of the remote

Re: [Rd] Determining the size of a package

2024-01-17 Thread Simon Urbanek
-release-macos-arm64/terra-00check.html Cheers, Simon > On Jan 18, 2024, at 12:26 PM, William Revelle wrote: > > Dear fellow developers, > > Is there an easy way to determine how big my packages (psych and psychTools) > will be on various versions of CRAN? > > I have bee

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

2024-01-10 Thread Simon Urbanek
only applies to the package library location, not to system tools. Cheers, Simon > On Jan 11, 2024, at 10:36 AM, Harmen Stoppels wrote: > > For context: I don't think Nix and Guix have to relocate anything, cause I > think they require absolute paths like /nix/store where all bi

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

2024-01-10 Thread Simon Urbanek
mmand -v built-in which is part of POSIX (where available - which is almost everywhere today) which would not require an external tool, but as noted I don't think this is the only problem Spack has... (and that's just core R - even a bigger can of worms with R packages :P). Cheers, Simon

Re: [Rd] Regenerate news feeds?

2023-11-17 Thread Simon Urbanek
Tim, thanks. I have updated R to the latest R-devel on the machine in the hope that is may help, but I suspect it will only affect new entries as they are generated progressively each day. Cheers, Simon > On Nov 18, 2023, at 11:38 AM, Tim Taylor > wrote: > > The news feeds (e

[Rd] GLFW [Was: Wayland Display Support in R Plot]

2023-10-29 Thread Simon Urbanek
ust fine. That said, both points were meant for the list in general - those are nice self-contained projects (add libwayland to Cairo and GLFW to rgl) for someone with spare time to contribute... Cheers, Simon > On 30/10/2023, at 9:48 AM, Duncan Murdoch wrote: > > On 29/10/2023 4

Re: [Rd] Wayland Display Support in R Plot

2023-10-29 Thread Simon Urbanek
ome GUI library for anything beyond that - so you may was well just run a Wayland-based browser and be done with it saving you all the bother (oh, right, that's called RStudio ;)). One package that may be worth adding Wayland backend to is rgl so you get OpenGL on Wayland - I'd simp

Re: [Rd] After package update, old S4 method is dispatched

2023-10-02 Thread Simon Urbanek
Jan, have you re-installed all packages? If you change (update) any package that uses S4 it may be necessary to re-install all its reverse-dependencies as well since they may include cached values in their namespaces, so the easiest is to make sure you re-install all packages. Cheers, Simon

Re: [Rd] Help requested: writing text to a raster in memory

2023-09-24 Thread Simon Urbanek
d scaling (in theory). Cheers, Simon > On 25/09/2023, at 2:01 PM, Duncan Murdoch wrote: > > I'm somewhat aware of how tricky it all is. For now I'm going to do it in R > (usng textshaping for layout and base graphics on the ragg::agg_capture > device to draw to the bitma

Re: [Rd] Help requested: writing text to a raster in memory

2023-09-24 Thread Simon Urbanek
r/src/cairotalk.c (the meat is in L608-) and for all but the drawing part there is an entire R package (in C++) devoted to this: https://github.com/r-lib/textshaping/tree/main/src -- Thomas Lin Pedersen is probably THE expert on this. Cheers, Simon > On 24/09/2023, at 7:44 AM, Duncan Murdoc

Re: [Rd] Detecting physical CPUs in detectCores() on Linux platforms

2023-08-07 Thread Simon Urbanek
> On 8/08/2023, at 12:07 PM, Dirk Eddelbuettel wrote: > > > On 8 August 2023 at 11:21, Simon Urbanek wrote: > | First, detecting HT vs cores is not necessarily possible in general, Linux > may assign core id to each HT depending on circumstances: > | > | $ grep &

Re: [Rd] Detecting physical CPUs in detectCores() on Linux platforms

2023-08-07 Thread Simon Urbanek
ical id",colnames(d))], `[`, 1))) which avoids subprocesses, quoting hell and all such issues... Cheers, Simon > On 8/08/2023, at 12:47 AM, Julian Hniopek wrote: > > On Mon, 2023-08-07 at 07:12 -0500, Dirk Eddelbuettel wrote: >> >> On 7 August 2023 at 08:48, Nils

Re: [Rd] Correct use of tools::R_user_dir() in packages?

2023-06-28 Thread Simon Urbanek
cific data, configuration and cache files in their respective user directories obtained from tools::R_user_dir(), provided that by default sizes are kept as small as possible and the contents are actively managed (including removing outdated material)." Cheers, Simon > On 28/06/2023

Re: [Rd] codetools wrongly complains about lazy evaluation in S4 methods

2023-06-13 Thread Simon Urbanek
default behavior in the generic itself (not necessarily a good idea) the default would be ncol = if (complete) nrow(qr.R(qr, TRUE)) else min(dim(qr.R(qr, TRUE))) to not rely on the internals of the implementation. Cheers, Simon > On 14/06/2023, at 6:03 AM, Kasper Daniel Hansen >

Re: [Rd] nightly r-devel.pkg builds failing since Jan 15

2023-02-26 Thread Simon Urbanek
Gabe, thanks, this was a fall-out from a power outage due to the cyclone. Although all systems were back up, svn lock files have led to an early abort in the update step. It should be fixed now. Cheers, Simon > On 27/02/2023, at 10:40 AM, Gabriel Becker wrote: > > Hi all, >

Re: [Rd] determine if `suppressMessages()` has been invoked

2023-02-19 Thread Simon Urbanek
) >= sizeof(msg)) memcpy(msg + sizeof(msg) - 4, "...", 4); Rmessage(msg); va_end(ap); } Cheers, Simon > On 20/02/2023, at 6:45 AM, Nino Hardt wrote: > > Awesome, this gets the job done. > > To answer your question: > When using C or C++ via Rinside or within

Re: [Rd] Question on non-blocking socket

2023-02-17 Thread Simon Urbanek
re quite complex matter - it's easy to get it wrong and create hard-to-detect bugs in you code unless you are an expert in it. It's one of the wheels you don't want to be reinventing. Cheers, Simon > On Feb 18, 2023, at 3:00 AM, Ben Engbers wrote: > > Hi Tomas, >

Re: [Rd] Sys.getenv(): Error in substring(x, m + 1L) : invalid multibyte string at '' if an environment variable contains \xFF

2023-01-30 Thread Simon Urbanek
t;, x, fixed = TRUE) : input string 2 is invalid in this locale so the rest of my comments stand ;). Thanks, Simon > On Jan 31, 2023, at 2:11 PM, Henrik Bengtsson > wrote: > > Thanks for the quick replies. > > For me, the main issue is that the value of an environment variabl

Re: [Rd] Sys.getenv(): Error in substring(x, m + 1L) : invalid multibyte string at '' if an environment variable contains \xFF

2023-01-30 Thread Simon Urbanek
hecks, we should make them conditional - even if the default is to add them. Again, the error is due to the implementation of Sys.getenv() breaking in R-devel, not due to any design decision. Cheers, Simon > On Jan 31, 2023, at 1:04 PM, Tomas Kalibera wrote: > > > On 1/30/23

Re: [Rd] patch about timezone name of China Standard Time on windows

2023-01-08 Thread Simon Urbanek
is better than current way? if it is i will try it in next 1-2 weeks. > I'm not sure how simple it would be to script this since others have been working on this, but if it was doable it would be a good start. There are others that know more about CLDR than I do. Cheers, Simon

Re: [Rd] patch about timezone name of China Standard Time on windows

2023-01-06 Thread Simon Urbanek
hed and changes have not broken something in R. So you can file an issue so this is on record, but I wouldn't include patches since they cannot be applied directly for reasons explained as it has to be done as a part of the full update, not just a single entry. Cheers, Simon > On Jan 6,

Re: [Rd] Repeated segfault at installing sysdata.rda with clang/san build

2022-12-18 Thread Simon Urbanek
it is trying to call a function which is a NULL pointer ... This is outside of R so really odd - perhaps some odd interaction of *SAN and glibc? No idea why it suddenly appeared - perhaps some changes in toolchain or glibc? Cheers, Simon > On 19/12/2022, at 8:41 AM, Dirk Eddelbuettel wrote

Re: [Rd] I do not want that R CMD build removes temp directory

2022-12-15 Thread Simon Urbanek
also use --no-test-load and the non-functional package will still be installed so you can inspect it. Cheers, Simon PS: please don't cross-post > On Dec 16, 2022, at 7:01 AM, Witold E Wolski wrote: > > I am getting a package build error, and can not figure out the problem.

Re: [Rd] RTools40 Error - sh: line 1: gcc: command not found

2022-11-28 Thread Simon Urbanek
Gene, I believe you have the wrong page - the link you listed is for an old version of R (4.0-4.1) - the current one (for 4.2.x) is https://cran.r-project.org/bin/windows/Rtools/rtools42/rtools.html Cheers, Simon > On 29/11/2022, at 7:39 AM, Gene Leynes wrote: > > Hello, > &

Re: [Rd] as.Date without "origin"

2022-11-03 Thread Simon Urbanek
h has not been finished yet. Cheers, Simon > On Nov 3, 2022, at 2:38 AM, Dan Dalthorp via R-devel > wrote: > > I don't see a compelling rationale for changing the default behavior as.Date > to deviate from the wholly reasonable status quo of "as.Date will accept

Re: [Rd] Lazy-evaluate elements wrapped with invisible

2022-10-30 Thread Simon Urbanek
. $m [1] 0.03834447 $plot_data [1] 1 2 3 > m2 <- { a(); a(); a() } > m2 computing... $m [1] 0.05177236 $plot_data [1] 1 2 3 But you cannot use the actual value without assigning it: > a()$m Error in a()$m : object of type 'promise' is not subsettable because R will not t

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

2022-10-15 Thread Simon Urbanek
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, > > It's very nice usage you provided here. May

Re: [Rd] Proposal to limit Internet access during package load

2022-09-26 Thread Simon Urbanek
ps it does make sense to exclude it. It would be pointless to appease the load check just to not be able to perform the function it was designed for... Cheers, Simon > On 27/09/2022, at 11:11 AM, Simon Urbanek wrote: > > > >> On 27/09/2022, at 11:02 AM, Gabriel Becker wrote

Re: [Rd] Proposal to limit Internet access during package load

2022-09-26 Thread Simon Urbanek
7; Calls: ... getBiocDevelVr -> getBiocYaml -> inet_handlers -> readLines Execution halted ERROR: loading failed So, yes, it does break. You should recover from the error and use a fall-back file that you ship. Cheers, Simon > Advice on what to do for the above use case that is be

Re: [Rd] Proposal to limit Internet access during package load

2022-09-26 Thread Simon Urbanek
> On 27/09/2022, at 10:21 AM, Iñaki Ucar wrote: > > On Mon, 26 Sept 2022 at 23:07, Simon Urbanek > wrote: >> >> Iñaki, >> >> I'm not sure I understand - system dependencies are an entirely different >> topic and I would argue a far more impo

Re: [Rd] Proposal to limit Internet access during package load

2022-09-26 Thread Simon Urbanek
nloads for binary dependencies which is an entirely different issue that needs a different solution (in a naive way declaring such dependencies, but we know it's not that simple - and download URLs don't help there). Cheers, Simon > On 27/09/2022, at 8:25 AM, Ucar wrote: > &g

Re: [Rd] Proposal to limit Internet access during package load

2022-09-26 Thread Simon Urbanek
t needed) - it is a common practice - have a look at sf (and other packages that copy projections data from PROJ). So, yes, that's a good argument for disallowing downloads to detect such issues in packages. Cheers, Simon > On 27/09/2022, at 9:02 AM, Gabriel Becker wrote: > >

Re: [Rd] Proposal to limit Internet access during package load

2022-09-26 Thread Simon Urbanek
> On Sep 27, 2022, at 8:25 AM, Iñaki Ucar wrote: > > On Sat, 24 Sept 2022 at 01:55, Simon Urbanek > wrote: >> >> Iñaki, >> >> I fully agree, this a very common issue since vast majority of server >> deployments I have encountered don't al

Re: [Rd] Proposal to limit Internet access during package load

2022-09-23 Thread Simon Urbanek
s Zenodo. This could be a matter of policy as opposed to the technical side above which would be adding such support to R CMD INSTALL. Cheers, Simon > On Sep 24, 2022, at 3:22 AM, Iñaki Ucar wrote: > > Hi all, > > I'd like to open this debate here, because IMO this is a big i

Re: [Rd] ...()

2022-08-27 Thread Simon Urbanek
..) as.list(substitute(.(...)))[-1] > str(f(a=g(),b)) List of 2 $ a: language g() $ : symbol b Cheers, Simon > On Aug 28, 2022, at 5:23 AM, Rui Barradas wrote: > > Hello, > > I don't believe it is documented but the best I could find was this not very > old r-devel thread

Re: [Rd] Floating point issue

2022-07-11 Thread Simon Urbanek
the original value even on M1), but it would be OS-specific. In the former R could impose its own guarantees - but currently it does not. Cheers, Simon [1] - https://github.com/r-devel/r-svn/blob/97c0a73f1758d09088c200f924d27b362d55ccdc/src/main/util.c#L2094 #include #include #include int

Re: [Rd] Rgui.exe: bug associated with non-ASCII characters

2022-05-19 Thread Simon Urbanek
(submitting a line without selection) was not since it truncated the line at the non-ASCII character. Cheers, Simon > On 20/05/2022, at 10:55 AM, Brodie Gaslam via R-devel > wrote: > > Is it possible you intended to use: > > c('pá', 'pé', 'pí', &#

Re: [Rd] calloc() vs. R_Calloc()

2022-04-07 Thread Simon Urbanek
Adrian, there are many more allocations in your code - for example, you're using resize() from utils.c which uses malloc/free so it will break since it's using the wrong allocator. You may need to replace *all* allocations in your project, not just some. Cheers, Simon > On 8/

[Rd] String interpolation [Was: string concatenation operator (revisited)]

2021-12-07 Thread Simon Urbanek
, but not sure if the complexity is worth it). Cheers, Simon > On Dec 8, 2021, at 12:56 AM, Taras Zakharko wrote: > > I fully agree! General string interpolation opens a gaping security hole and > is accompanied by all kinds of problems and decisions. What I envision > in

Re: [Rd] string concatenation operator (revisited)

2021-12-07 Thread Simon Urbanek
curity hole and has questionable semantics (where you evaluate etc). Hence it's much easier to ban a package than to hack it out of R ;). Cheers, Simon > — Taras > > >> On 7 Dec 2021, at 02:27, Avi Gross via R-devel wrote: >> >> After seeing what others are s

Re: [Rd] capturing multiple warnings in tryCatch()

2021-12-02 Thread Simon Urbanek
foo() ..- attr(*, "class")= chr [1:3] "simpleWarning" "warning" "condition" $ :List of 2 ..$ message: chr "warning 2" ..$ call : language foo() ..- attr(*, "class")= chr [1:3] "simpleWarning" "warning" "conditio

Re: [Rd] FLIBS in MacOS M1 binary at odds with documentation for optional libraries/tools

2021-11-01 Thread Simon Urbanek
Naras, thanks. It seems that the FLIBS check resolves symlinks, unfortunately (all others are fine). I would like to remind people that reports are a lot more useful *before* the release - that's why we publish RCs. Thanks, Simon > On Nov 2, 2021, at 3:03 PM, Balasubramanian Na

Re: [Rd] parallel PSOCK connection latency is greater on Linux?

2021-11-01 Thread Simon Urbanek
tions=\"no-delay\")'") > (x <- microbenchmark(clusterEvalQ(cl, iris), times = 100, unit = "us")) Unit: microseconds exprmin lq mean median uq max neval clusterEvalQ(cl, iris) 112.41 115.33 128.9988 117.3065 120.5385 348.702

Re: [Rd] Is it a good choice to increase the NCONNECTION value?

2021-08-25 Thread Simon Urbanek
criptors may be used. Anyway, I think the take away was that likely the best way forward is to make it configurable at startup time with possible option to check that value against the feasibility of open connections. Cheers, Simon > On Aug 26, 2021, at 9:00 AM, GILLIBERT, Andre &

Re: [Rd] [External] Re: Is it a good choice to increase the NCONNECTION value?

2021-08-24 Thread Simon Urbanek
up to raise it to 1024 by default regardless of the ulimit -n setting (comments say this is for DLLs). I guess based on that we know at least what to expect so we could trivially warn if the new setting is larger that the user limit. Cheers, Simon > On Aug 25, 2021, at 1:45 PM, luke-tier...@u

Re: [Rd] Is it a good choice to increase the NCONNECTION value?

2021-08-24 Thread Simon Urbanek
t the very least increasing the limit significantly (at least 1k if not more) and, ideally, make it dynamic if memory footprint is an issue. Cheers, Simon > On Aug 25, 2021, at 8:53 AM, Martin Maechler > wrote: > >>>>>> GILLIBERT, Andre >>>&g

Re: [Rd] [External] Re: Update on rtools4 and ucrt support

2021-08-23 Thread Simon Urbanek
x27;ll leave it to the Windows experts to address the details and work together. Cheers, Simon > On Aug 24, 2021, at 10:03 AM, Avraham Adler wrote: > > > Thank you, Simon. That was valuable. Skimming that quickly, I get a bit > concerned. I’ve been building from source and then us

Re: [Rd] [External] Re: Update on rtools4 and ucrt support

2021-08-23 Thread Simon Urbanek
is in https://svn.r-project.org/R-dev-web/trunk/WindowsBuilds/winutf8/ucrt3/howto.html <https://svn.r-project.org/R-dev-web/trunk/WindowsBuilds/winutf8/ucrt3/howto.html> Cheers, Simon > On Aug 24, 2021, at 8:34 AM, Avraham Adler wrote: > > On Mon, Aug 23, 2021 at 11:09 PM wrote:

Re: [Rd] Force quitting a FORK cluster node on macOS and Solaris wreaks havoc

2021-08-12 Thread Simon Urbanek
g master's exit handlers etc. That's why the children have to use either abort or mcexit() to terminate - which is what mcparallel() does. If you use q() a lot of things go wrong no matter the platform - e.g. try using ? in the master session after sourcing your code. Cheers, Simon &

Re: [Rd] Double to uint64_t on M1

2021-08-11 Thread Simon Urbanek
ur subject doesn't match your question as the uint64_t conversion is well-defined and the same on both platforms, but the conversion to int64_t in undefined. Cheers, Simon > On 12/08/2021, at 10:50 AM, Dipterix Wang wrote: > > Hi, > > I was trying to convert REALSXP to

Re: [Rd] attach "warning" is a message

2021-08-09 Thread Simon Urbanek
wo options are to clarify the documentation (also in library()) or change to a warning - not sure what the consequences of the latter would be. Cheers, Simon > On 10/08/2021, at 2:06 AM, Barry Rowlingson > wrote: > > If I mask something via `attach`: > >> d = data.f

Re: [Rd] On read.csv and write.csv

2021-07-01 Thread Simon Urbanek
. Note that such CSV files can be read in R by read.csv(file = "", row.names = 1) Cheers, Simon > On 2/07/2021, at 10:29 AM, Gabriel Becker wrote: > > > > On Thu, Jul 1, 2021 at 1:46 PM Stephen Ellison wrote: > > Please run the reproducible example provide

Re: [Rd] On read.csv and write.csv

2021-06-30 Thread Simon Urbanek
row.names=FALSE. Cheers, Simon PS: this is likely a question for R-help rather than R-devel > On 1/07/2021, at 9:15 AM, Stephen Ellison wrote: > > Apologies if this is a well-worn question; I haven’t found it so far but > there's a lot of r-dev and I may have missed it in t

Re: [Rd] S3 weirdness

2021-06-24 Thread Simon Urbanek
S3 method dispatch tables: > methods(as.ts) [1] as.ts.default* as.ts.zoo* as.ts.zooreg* see '?methods' for accessing help and source code so the behavior is as expected. Cheers, Simon > On 25/06/2021, at 9:56 AM, Gabor Grothendieck wrote: > > If we start up a vanilla ses

Re: [Rd] [External] Possible ALTREP bug

2021-06-16 Thread Simon Urbanek
the value itself as one would expect. Cheers, Simon > On Jun 17, 2021, at 2:22 AM, Toby Hocking wrote: > > By the way, where is the documentation for INTEGER_ELT, REAL_ELT, etc? I > looked in Writing R Extensions and R Internals but I did not see any > mention. > REAL_ELT is

Re: [Rd] Feature request – math in HTML help

2021-05-27 Thread Simon Urbanek
kages which is already possible and a solved problem as Duncan pointed out. You can write R documentation which uses MathJax in your package, but you cannot render existing R documentation with MathJax (currently, if I understand that correctly). I hope this clarifies things a bit. Cheers,

Re: [Rd] R Console Bug?

2021-04-17 Thread Simon Urbanek
Just for completeness, This can be easily illustrated simply in R, no C code needed: cat("foo\n\rbar\n") In unix terminal: > cat("foo\n\rbar\n") foo bar In Mac-GUI: > cat("foo\n\rbar\n") bar Cheers, Simon > On Apr 17, 2021, at 20:29, Simon Urban

Re: [Rd] R Console Bug?

2021-04-17 Thread Simon Urbanek
data chunk %d of 3\n ",k+1); Which makes sure the \n is interpreted as \r\n first and only then you follow with \r. I suppose we could sunset the special handling of \r since it is likely quite rare to see Mac line endings these days... you could file an issue against Mac-GUI. Cheers, Simon

Re: [Rd] R Console Bug?

2021-04-16 Thread Simon Urbanek
ent anywhere but in Terminal by definition). Can you clarify what the code tries to trigger? Cheers, Simon > On Apr 16, 2021, at 23:11, Morgan Morgan wrote: > > Hi, > > I am getting a really weird behaviour with the R console. >

Re: [Rd] custom allocators, Valgrind and uninitialized memory

2021-04-14 Thread Simon Urbanek
semantics are since you are the author of the custom allocator. Does that make sense? Cheers, Simon > On Mar 30, 2021, at 18:27, Andreas Kersting wrote: > > Hi Simon, > > Yes, if this was acceptable on CRAN, I would agree that calling > VALGRIND_MAKE_MEM_DEFINED() in

Re: [Rd] custom allocators, Valgrind and uninitialized memory

2021-04-14 Thread Simon Urbanek
Andres, correct me if I'm wrong, but the issue here is not initialisation but rather valgrind flagging. You simply have to call VALGRIND_MAKE_MEM_DEFINED() in your code after allocVector3() to declare that you have initialised the memory - or am I missing something? Cheers, Simon &g

Re: [Rd] boneheaded BLAS questions

2021-03-17 Thread Simon Urbanek
x27;t work. Dirk has the luxury of having control over what he compiles, but that is not always the case (like with Accelerate or MKL) ... Cheers, Simon > On 18/03/2021, at 3:53 PM, Ben Bolker wrote: > > Thanks. I know it's supposed to Just Work (and I definitely appreci

Re: [Rd] inheritance and attach

2021-03-15 Thread Simon Urbanek
register them using .S3method(). Without registration you have to load them into the global env for them to work since this is now the only environment that doesn't require registration. Cheers, Simon > On Mar 16, 2021, at 7:19 AM, Therneau, Terry M., Ph.D. via R-devel > wrote: >

Re: [Rd] An argument promise containing bytecode?

2021-03-07 Thread Simon Urbanek
Taras, I don't think this has anything to do with promises, rather it is called Just-In-Time (JIT) compilation - see ?enablleJIT in R, it is enabled by default, so the function will be compiled on second use. Cheers, Simon > On Mar 7, 2021, at 11:12 PM, Taras Zakharko wrote: >

Re: [Rd] Apple M1 CRAN checks

2021-02-28 Thread Simon Urbanek
0000e+00 0.000e+00 -1.0658141036401502788e-14 [4] -3.5527136788005009294e-15 I hope this helps you to track it down. Cheers, Simon > On Mar 1, 2021, at 4:50 AM, Paul Gilbert wrote: > > If there was a response to the "how can I test it out" par

Re: [Rd] Checking multiple inheritance of S4 objects using R's C API

2021-02-15 Thread Simon Urbanek
ich allows you to get the list of superclasses for S4 objects, but according to the definition of some people it is not part of the official R API so your mileage may vary. Cheers, Simon > On Feb 16, 2021, at 12:03 PM, Emre Gonulates wrote: > > Hi, > > Suppose I have the f

Re: [Rd] Request for a crop option on R's standard plot context menu

2021-02-12 Thread Simon Urbanek
that route. Cheers, Simon > On Feb 12, 2021, at 5:55 AM, Marthews, Toby R. via R-devel > wrote: > > Dear R Dev, > > I hope you don't mind a request for a feature from a long-time R user > (happily using R since 2005). > > I use R for lots of plotting for my

Re: [Rd] Unexpected behavior with inheritance and using S3 classes as slots in S4 class

2021-01-28 Thread Simon Urbanek
: [1] "world" attr(,"class") [1] "b" "a" Cheers, Simon > On Jan 28, 2021, at 15:55, Ezra Tucker wrote: > > Hi all, > > I have a situation where I'm trying to use S3 classes as slots in an S4 class > and am running into some pr

Re: [Rd] parallel PSOCK connection latency is greater on Linux?

2020-11-03 Thread Simon Urbanek
there is any other way we could infer the intention of the user to try to choose the right approach... Cheers, Simon > On Nov 3, 2020, at 02:28, Jeff wrote: > > Could TCP_NODELAY and TCP_QUICKACK be exposed to the R user so that they > might determine what is best for their

Re: [Rd] parallel PSOCK connection latency is greater on Linux?

2020-11-01 Thread Simon Urbanek
+ R but with TCP_NODELAY enabled in R_SockConnect(): Unit: microseconds expr min lq mean median uq max neval clusterEvalQ(cl, iris) 156.125 166.41 180.8806 170.247 174.298 5322.234 1000 Cheers, Simon > On 2/11/2020, at 3:39 AM, Jeff wrote: >

Re: [Rd] New URL redirect checks

2020-09-16 Thread Simon Urbanek
heers, Simon > On Sep 17, 2020, at 5:35 AM, Gábor Csárdi wrote: > > Dear all, > > the new CRAN URL checks flag HTTP 301 redirects. While I understand > the intent, I think this is unfortunate, because several URL shortener > services use 301 redirects, and often a shorter URL

Re: [Rd] CRAN metadata broken?

2020-09-15 Thread Simon Urbanek
$ ls -l stringi* -rw-r--r-- 1 pkgbuild admin 13641892 Sep 10 06:29 stringi_1.5.3.tgz so I guess there was a new version and the CRAN sync didn't finish yet when Gábor checked? Cheers, Simon [PS: please consider using CRAN or R-SIG-Mac since this is not related to R development.] >

Re: [Rd] Managing unix signal in R

2020-08-14 Thread Simon Urbanek
What do you mean by "manage unix signal"? The main signals like INT, PIPE or SEGV are handled by R and are not exposed to the user code. What exactly do you intend to do? Cheers, Simon > On Aug 14, 2020, at 6:44 PM, neonira Arinoem wrote: > > Hello > > Just wonde

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