Re: [Rd] compile c++ code in an R package without -g

2016-10-16 Thread Simon
B_CXXFLAGS) $(CXX1XFLAGS:-g=) $(CXX1XSTD) all: $(SHLIB) %.o: %.cpp $(SHLIB_CXX1XLD) $(wsrf_FLAGS) -c $< -o $@ However, I am not sure if it is allowed on CRAN, and I think it must have a reason for that, though I don't know. So I didn't do that in my package. Best reg

[Rd] How to make an R package that uses Boost.Thread, qualified to be published on CRAN or shared by the most

2013-11-03 Thread Simon
.) Simon PS: Below are the source files and results of my tries for exploring BOOSTLIB on win-builder, please forgive me use win-builder as a test machine, so I post my questions here. The test package is derived from command Rscript -e "Rcpp.package.skeleton()", below just

Re: [Rd] How to make an R package that uses Boost.Thread, qualified to be published on CRAN or shared by the most

2013-11-03 Thread Simon
Hi Dirk, Thank you very much, your answers are always helpful and point me to the right direction. And I also hope the C++11 proposal ( https://stat.ethz.ch/pipermail/r-devel/2013-October/067677.html) will be approved soon. :-) Simon On 11/03/2013 09:54 PM, Dirk Eddelbuettel wrote: > O

Re: [Rd] Bugzilla down?

2019-02-25 Thread Simon Urbanek
I do. The server ran out of disk earlier today and it seems that it killed bugzilla somehow. I'll have a look. Thanks, Simon > On Feb 25, 2019, at 2:07 PM, Gabriel Becker wrote: > > Hi Martin (who I believe manages bz?) et al., > > I'm getting 503 Service Unavailabl

Re: [Rd] Bugzilla down?

2019-02-25 Thread Simon Urbanek
Ok, fixed. Simon > On Feb 25, 2019, at 2:45 PM, Simon Urbanek > wrote: > > I do. The server ran out of disk earlier today and it seems that it killed > bugzilla somehow. I'll have a look. > Thanks, > Simon > > >> On Feb 25, 2019, at 2:07 PM, Gabriel

Re: [Rd] Exit status of Rscript

2019-02-28 Thread Simon Urbanek
> system2("Rscript", c("-e", shQuote("stop('foo')"))) == 0 Error: foo Execution halted [1] FALSE > sessionInfo() R version 3.5.2 (2018-12-20) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: OS X El Capitan 10.11.6 > system2("Rscript", c("-e", shQuote("stop('foo')"))) == 0 Error: foo Ex

Re: [Rd] Exit status of Rscript when setting options(error=utils::recover)

2019-03-18 Thread Simon Urbanek
As Tomas pointed out, it may be helpful to read the R documentation. The error option expects a function, so I suppose you intended something like options(error=function() {recover(); q(status=1)}) which corresponds to calling dump.frames() Cheers, Simon > On Mar 17, 2019, at 23:44, comic f

Re: [Rd] Use of C++ in Packages

2019-03-29 Thread Simon Urbanek
rily lack of tools, it is lack of knowledge - which is why I think Tomas' post is so important. Cheers, Simon > On Mar 29, 2019, at 11:19 AM, Jim Hester wrote: > > First, thank you to Tomas for writing his recent post[0] on the R > developer blog. It raised important

Re: [Rd] Use of C++ in Packages

2019-03-29 Thread Simon Urbanek
of C++ with R. > Well, unless someone actually takes the initiative there is no reason to believe in a bright future of C++. As we have seen with the lack of adoption of CXXR (which I thought was an incredible achievement), not enough people seem to really care about C++. If that is not true,

Re: [Rd] SUGGESTION: Settings to disable forked processing in R, e.g. parallel::mclapply()

2019-04-12 Thread Simon Urbanek
r, but not all packages do it which means you can hit forked code without knowing it. If you use mclapply() in user code, you typically know what you're doing, but if a package author does it for you, it's a different story. Cheers, Simon > On Apr 12, 2019, at 21:50, Kevin Ushey wro

Re: [Rd] SUGGESTION: Settings to disable forked processing in R, e.g. parallel::mclapply()

2019-04-13 Thread Simon Urbanek
will share memory as long as possible. It is rather obvious that any new objects you create can no longer be shared as they now exist separately in each process. Cheers, Simon > On Apr 13, 2019, at 06:05, Iñaki Ucar wrote: > > On Sat, 13 Apr 2019 at 03:51, Kevin Ushey wrote: >&

Re: [Rd] SUGGESTION: Settings to disable forked processing in R, e.g. parallel::mclapply()

2019-04-13 Thread Simon Urbanek
> On Apr 13, 2019, at 16:56, Iñaki Ucar wrote: > > On Sat, 13 Apr 2019 at 18:41, Simon Urbanek > wrote: >> >> Sure, but that a completely bogus argument because in that case it would >> fail even more spectacularly with any other method like PSOCK because yo

Re: [Rd] Background R session on Unix and SIGINT

2019-04-30 Thread Simon Urbanek
evaluation. Cheers, Simon > On Apr 30, 2019, at 3:44 PM, Gábor Csárdi wrote: > > Hi All, > > I realize that this is not a really nice reprex, but anyone has an > idea why a background R session would "remember" an interrupt (SIGINT) > on Unix? > > rs <

Re: [Rd] Background R session on Unix and SIGINT

2019-04-30 Thread Simon Urbanek
Can you give an example without callr? The key is how is the process stated and what it is doing which is entirely opaque in callr. Windows doesn't have signals, so the process there is entirely different. Most of the WIN32 processing is event-based. Cheers, Simon > On Apr 30, 2019,

Re: [Rd] [External] Re: Background R session on Unix and SIGINT

2019-05-01 Thread Simon Urbanek
g you can either just run R_CheckUserInterrupt() explicitly, or on R side do anything that does that, e.g. to take your example "tryCatch(Sys.sleep(0), interrupt = function(e) e)" will clear it. Cheers, Simon > On Apr 30, 2019, at 7:03 PM, Gábor Csárdi wrote: > > Unfort

Re: [Rd] Pcre install

2019-05-14 Thread Simon Urbanek
sudo apt-get install libpcre3-dev please read the docs [R-admin: A.1 Essential programs and libraries] - you may be missing more dependencies > On May 14, 2019, at 9:44 AM, yueli wrote: > > Hello, > > > > I downloaded R-3.6.0.tar.gz from https://cran.r-project.org/src/base/R-3/. > > > I

Re: [Rd] most robust way to call R API functions from a secondary thread

2019-05-20 Thread Simon Urbanek
synchronize on R API calls which are likely a small fraction on the entire time while you keep all threads alive. His question was how to do that safely. (BTW: I really like the touch of counting frames that toplevel exec can use ;) - it may make sense to deal with that edge-case in R if we can

Re: [Rd] Race condition on parallel package's mcexit and rmChild

2019-05-20 Thread Simon Urbanek
Because that's the communication protocol between the parent and child. There is a difference between unsolicited exit and empty result exit. Cheers, Simon > On May 20, 2019, at 11:22 AM, Sun Yijiang wrote: > > Have read the latest code, but I still don't understand why

Re: [Rd] HTTPS warning on developer.r-project.org

2019-05-22 Thread Simon Urbanek
More to the point: the custom search function is currently broken anyway - it just gives me 404. Should we just get rid of it? If people want to use Google they can just say site:developer.r-project.org foo > On May 22, 2019, at 1:08 AM, Paul Menzel wrote: > > [Please CC me on replies, as

Re: [Rd] Possible bug when finding shared libraries during staged installation

2019-05-24 Thread Simon Urbanek
I'll have a look at the code - I don't think I actually reviewed all those macOS modifications - I wasn't even aware that they were added to the code. > On May 24, 2019, at 08:52, Martin Maechler wrote: > >> Kara Woo >>on Thu, 23 May 2019 14:24:26 -0700 writes: > >> Hi all, >> Wi

Re: [Rd] use of buffers in sprintf and snprintf

2019-05-30 Thread Simon Urbanek
eof(tempname)) Rf_error("file name is too long"); BTW: most OSes systems have a path limits that are no lower than 256 so you should allow at least as much. Cheers, Simon > On May 29, 2019, at 11:49 AM, jing hua zhao wrote: > > Dear R-developers, > > I am struggli

Re: [Rd] Offer zip builds

2019-06-07 Thread Simon Urbanek
Just to add to that point - it is expected that the registry is appropriately updated so the correct version of R can be located. Just unpacking a ZIP won't work in general since tools using R have no reliable way to find it. Cheers, Simon > On Jun 6, 2019, at 6:33 AM, Jeroen Oom

Re: [Rd] R C API resize matrix

2019-06-17 Thread Simon Urbanek
es of TRUELENGTH so not sure where we stand now (shortened vectors used to fool the garbage collector as far as object sizes go). I wouldn't do it unless you're dealing with rally huge matrices. Cheers, Simon > On Jun 14, 2019, at 5:31 PM, Morgan Morgan wrote: > > Hi, > &

Re: [Rd] possible bug in R's configure check for C++11 features

2019-09-03 Thread Simon Urbanek
Kasper, I haven’t checked in depth, so just to clarify: you *are* setting CXX11=g++ so it is doing what you asked it to. Since the settings are inherited upwards, this implies that you are setting both CXX14 and CXX17 to g++. So I’m not quite sure I understand your concern. Cheers, Simon

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

2019-11-01 Thread Simon Urbanek
Note that your desire is by definition impossible - as your example also shows checking for S4 inheritance involves evaluation and thus allocation which cannot be avoided by the dynamic design of S4 inheritance. Cheers, Simon > On Nov 1, 2019, at 9:23 AM, Jan Gorecki wrote: > >

Re: [Rd] running R with users home dirs on a shared filesystems

2019-12-13 Thread Simon Urbanek
() - it is technically against CRAN policies but we have seen it in the wild. Cheers, Simon > On Dec 13, 2019, at 1:36 PM, lejeczek via R-devel > wrote: > > Hi guys, > > I want to ask devel for who knows better - having multiple > nodes serving users home dirs off th

Re: [Rd] Inconsistent behavior for the C AP's R_ParseVector() ?

2019-12-14 Thread Simon Urbanek
ded R). There are many different errors, your is just one of many that can occur - any R API call that does allocation (and parsing obviously does) can cause errors. Note that this is true for pretty much all R API functions. Cheers, Simon > On Dec 14, 2019, at 11:25 AM, Laurent Gautie

Re: [Rd] Inconsistent behavior for the C AP's R_ParseVector() ?

2019-12-14 Thread Simon Urbanek
Laurent, > On Dec 14, 2019, at 5:29 PM, Laurent Gautier wrote: > > Hi Simon, > > Widespread errors would have caught my earlier as the way that code is > using only one initialization of the embedded R, is used quite a bit, and > is covered by quite a few unit te

Re: [Rd] Downsized R configuration for flat deployment

2019-12-22 Thread Simon Urbanek
e flat by default so please clarify what you mean. It's easy to create completely dynamic R deployment - and easy to install packages - both binary and from sources. Cheers, Simon > On Dec 21, 2019, at 8:39 AM, dme...@gmail.com wrote: > > Dear folks, > > I'm testing a d

Re: [Rd] SUGGESTION: Settings to disable forked processing in R, e.g. parallel::mclapply()

2020-01-10 Thread Simon Urbanek
easily implemented in a package so R doesn’t need to be modified. Cheers, Simon Sent from my iPhone >> On Jan 10, 2020, at 04:34, Tomas Kalibera wrote: >> >> On 1/10/20 7:33 AM, Henrik Bengtsson wrote: >> I'd like to pick up this thread started on 2019-04-11 >

Re: [Rd] SUGGESTION: Settings to disable forked processing in R, e.g. parallel::mclapply()

2020-01-10 Thread Simon Urbanek
ng or stop on fork, it doesn't have to be part of core R, there are other packages that use fork() as well, so what I proposed is much safer than hacking the parallel package. Cheers, Simon > On Jan 10, 2020, at 10:58 AM, Henrik Bengtsson > wrote: > > The RStudio GUI w

Re: [Rd] SUGGESTION: Settings to disable forked processing in R, e.g. parallel::mclapply()

2020-01-10 Thread Simon Urbanek
e documentation. As I said, if you have some software that embeds R and has issue with forks, then that software should be use pthread_atfork() to control the behavior. Cheers, Simon > On Jan 10, 2020, at 3:34 PM, Henrik Bengtsson > wrote: > > On Fri, Jan 10, 2020 at 11:2

Re: [Rd] SUGGESTION: Settings to disable forked processing in R, e.g. parallel::mclapply()

2020-01-10 Thread Simon Urbanek
> On Jan 10, 2020, at 3:10 PM, Gábor Csárdi wrote: > > On Fri, Jan 10, 2020 at 7:23 PM Simon Urbanek > wrote: >> >> Henrik, >> >> the example from the post works just fine in CRAN R for me - the post was >> about homebrew build so it's concei

Re: [Rd] SUGGESTION: Settings to disable forked processing in R, e.g. parallel::mclapply()

2020-01-10 Thread Simon Urbanek
> On Jan 10, 2020, at 3:10 PM, Gábor Csárdi wrote: > > On Fri, Jan 10, 2020 at 7:23 PM Simon Urbanek > wrote: >> >> Henrik, >> >> the example from the post works just fine in CRAN R for me - the post was >> about homebrew build so it's concei

Re: [Rd] R CMD INSTALL cannot recognize full path on Windows

2020-03-11 Thread Simon Urbanek
licate the issue with the GH package you created. Cheers, Simon * installing *source* package 'testPackage' ... ** using staged installation ** libs *** arch - i386 echo "test1 is [1] 0.1522111 0.2533619 0.6591809" test1 is [1] 0.1522111 0.2533619 0.6591809 echo "R_HOM

Re: [Rd] pipe(): input to, and output from, a single process

2020-03-16 Thread Simon Urbanek
FWIW if you're on unix, you can use named pipes (fifos) for that: > system("mkfifo my.output") > p = pipe("sed -l s:hello:oops: > my.output", "w") > i = file("my.output", "r", blocking=FALSE, raw=TRUE) > writeLines("hello

Re: [Rd] help with rchk warnings on Rf_eval(Rf_lang2(...))

2020-03-23 Thread Simon Urbanek
Ben, yes, you have to store the result into a variable, then unprotect, then return. Cheers, S > On 24/03/2020, at 10:07 AM, Ben Bolker wrote: > > > Thanks, that's really useful. One more question for you, or someone > else here: > > const ArrayXd glmLink::linkFun(const ArrayXd& mu) const

Re: [Rd] Rebuilding and re-checking of downstream dependencies on CRAN Mac build machines

2020-03-26 Thread Simon Urbanek
any actual leads, please post them. The CRAN machine uses the tools that are available on CRAN: https://cran.r-project.org/bin/macosx/tools/ (clang-7 and gfortran-6.1 for 3.6.x) Cheers, Simon > On 27/03/2020, at 7:38 AM, Winston Chang wrote: > > I have two questions about t

Re: [Rd] status of Java & rJava?

2020-03-28 Thread Simon Urbanek
rs to upgrade. Cheers, Simon > On 29/03/2020, at 9:18 AM, Spencer Graves wrote: > > Hello, All: > > > Is Java being deprecated for R? > > > I ask, because I've been unable to get rJava 0.9-11 to work under > either macOS 10.15 or Windows 10,

Re: [Rd] [BULK] Re: status of Java & rJava?

2020-03-28 Thread Simon Urbanek
-project.org as mirror since there was a hiccup with macOS sync across mirrors). Cheers, Simon > On 29/03/2020, at 4:29 PM, Spencer Graves wrote: > > Hi, Simon et al.: > > > My attempts to install rJava 0.9-12 from source failed under both macOS > 10.15.4 and Windows

Re: [Rd] suggestion: "." in [lsv]apply()

2020-04-16 Thread Simon Urbanek
r alarm bells that something is wrong ;). You can certainly write a new function that uses a different syntax (and I'm sure someone has already done that in the package space), but what you propose is incompatible with *apply in R (and very much not R syntax). Cheers, Simon > To illustra

Re: [Rd] suggestion: "." in [lsv]apply()

2020-04-16 Thread Simon Urbanek
ual proposal, not general ideas about syntax improvement. Cheers, Simon > On 17/04/2020, at 3:53 AM, Sokol Serguei wrote: > > Simon, > > Thanks for replying. In what follows I won't try to argue (I understood that > you find this a bad idea) but I would like to mak

Re: [Rd] R not running under lldb? (osx)

2020-04-21 Thread Simon Urbanek
non-release binaries that are not notarized and install them by hand, e.g.: curl -L http://mac.r-project.org/high-sierra/R-4.0-branch/x86_64/R-4.0-branch.tar.gz | tar fxz - -C / Of course, this disables the Apple protections and thus is not recommended for casual users. Cheers, Simon * - more

Re: [Rd] R not running under lldb? (osx)

2020-04-21 Thread Simon Urbanek
Tim, sure, make sense (it's also easier to use ASAN and friends that way). The only issue is that it won't work for mcOS-specific bugs. Cheers, Simon > On 22/04/2020, at 3:55 PM, Tim Keitt wrote: > > Thanks Simon. I'll probably just switch to rocker when needing

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

2020-04-28 Thread Simon Urbanek
Sorry, the code works perfectly fine for me in R even for 1e6 observations (but I was testing with R 4.0.0). Are you using some kind of GUI? Cheers, Simon > On 28/04/2020, at 8:11 PM, Shian Su wrote: > > Dear R-devel, > > I am experiencing issues with running GAM models usi

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

2020-04-28 Thread Simon Urbanek
s small, or you need to read it first, then other methods like PSOCK may be preferable. In any case, parallelization only makes sense for code that you know will take a long time to run. Cheers, Simon > On 29/04/2020, at 11:54 AM, Shian Su wrote: > > Thanks Henrik, > > That cle

Re: [Rd] "not a valid win32 application" with rtools40-x86_65.exe on Windows 10

2020-04-29 Thread Simon Urbanek
Are you missing the 32-bit Java JDK? Cheers, S > On 30/04/2020, at 4:37 PM, Spencer Graves wrote: > > Hello, All: > > > "00install.out" from "R CMD check Ecfun_0.2-4.tar.gz" includes: > > > Error: package or namespace load failed for 'Ecfun': > .onLoad failed in loadNamespace() for

Re: [Rd] "not a valid win32 application" with rtools40-x86_65.exe on Windows 10

2020-05-02 Thread Simon Urbanek
ave to do it by hand and the instructions it gives you are not working for the command shell. Cheers, Simon > On 1/05/2020, at 4:51 PM, Spencer Graves wrote: > > Hi, Jeroen et al.: > > > On 2020-04-30 03:15, Jeroen Ooms wrote: >> On Thu, Apr 30, 2020 at 6:38

Re: [Rd] defining r audio connections

2020-05-07 Thread Simon Urbanek
is solely at CRAN's discretion to decide what gets published, so it may be worth raising it with the team, ask for the reasons and what it would take for them to accept packages using that API. Cheers, Simon > On 8/05/2020, at 1:02 AM, Jim Hester wrote: > > https://github.com/j

Re: [Rd] GCC warning

2020-05-22 Thread Simon Urbanek
don't see any link to what you submitted so can’t look at the code involved. Cheers, Simon > On May 22, 2020, at 7:25 PM, Adrian Dușa wrote: > > I am trying to submit a package on CRAN, and everything passes ok on all > platforms but Debian, where CRAN responds with an autom

Re: [Rd] r-project.org SSL certificate issues

2020-06-09 Thread Simon Urbanek
To be clear, this not an issue in the libraries nor R, the certificates on the server were simply wrong. So, no, this has nothing to do with R. Cheers, Simon > On Jun 10, 2020, at 10:45 AM, Henrik Bengtsson > wrote: > > Was this resolved upstream or is this something that R

Re: [Rd] r-project.org SSL certificate issues

2020-06-09 Thread Simon Urbanek
that R is likely not used for sensitive transactions, but I would rather it warned me about situations where the communication may be compromised instead of just silently going along. Cheers, Simon > On Jun 10, 2020, at 11:39 AM, peter dalgaard wrote: > > Yes and no... At least

Re: [Rd] tcltk image reading problem (on a mac?): [tcl] encountered an unsupported criticial chunk type "eXIf"

2020-06-11 Thread Simon Urbanek
, but not for wish. Back to the original question - do you have any example of a file that doesn't work so I could test? Exif chunks are fairly rare in PNG and are a more late extension so I couldn't find any examples. Thanks, Simon > On 12/06/2020, at 12:24 PM, Wayne Oldford wrote:

Re: [Rd] tcltk image reading problem (on a mac?): [tcl] encountered an unsupported criticial chunk type "eXIf"

2020-06-11 Thread Simon Urbanek
d simply remove any offending chunks with writePNG("test.png",readPNG("exIf.png", TRUE,TRUE)) then the output work with tcltk. Cheers, Simon > On 12/06/2020, at 1:00 PM, Simon Urbanek wrote: > > Wayne, > > that one is unrelated, but interesting - you ca

Re: [Rd] tcltk image reading problem (on a mac?): [tcl] encountered an unsupported criticial chunk type "eXIf"

2020-06-12 Thread Simon Urbanek
ian Ripley wrote: > >> On 12/06/2020 03:49, Fox, John wrote: >> Dear Simon, >>> On Jun 11, 2020, at 9:00 PM, Simon Urbanek >>> wrote: >>> >>> Wayne, >>> >>> that one is unrelated, but interesting - you can fix it with >>>

Re: [Rd] Speed-up/Cache loadNamespace()

2020-07-19 Thread Simon Urbanek
Rscript call with a very tiny Rserve client program which just calls source(""). I can give you more details if you're interested. Cheers, Simon * - there are some packages that are inherently incompatible with fork() - e.g. you cannot fork Java JVM or open connections. > On

Re: [Rd] Invisible names problem

2020-07-22 Thread Simon Urbanek
ases (what if you duplicated the wrapper and thus there were multiple wrappers referencing it?) and not sure if it has a way to find out. The other way to deal with that would be at serialization time if it could be detected such that it can remove the wrapper. Since the intersection of serialization expert

Re: [Rd] Experimental CI tool for R

2020-07-23 Thread Simon Urbanek
kages. Cleary we could just fork it, but I guess it would make more sense if this was a coordinated effort. Cheers, Simon > On Jul 21, 2020, at 23:55, Jeroen Ooms wrote: > > Based on ideas from the R-core discussion panel at useR2020, I created > a little CI tool to make it easier to fo

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

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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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?

2021-04-17 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] 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] [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] 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] 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] 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] 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] 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] 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] [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] [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] 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: 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?

2021-08-25 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] 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] 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] CRAN: MacOS X binary: not available, see check log?

2010-04-15 Thread Simon Urbanek
as binaries, so the migration can take a day or two ;). Cheers, Simon > The R.oo package is listed as "MacOS X binary: not available, see > check log?", but the 'check log' show no errors > URL: http://cran.r-project.org/web/packages/R

Re: [Rd] R CMD check tells me 'no visible binding for globalvariable ', what does it mean?

2010-04-16 Thread Simon Urbanek
e warnings you cannot eliminate (for example because you believe them to be spurious) send an explanatory note with your submission." It talks explicitly about warnings, notes are not mentioned at all... That said, you should examine all notes and make sure they are not indications of probl

Re: [Rd] grid.cap() requires more time?

2010-04-17 Thread Simon Urbanek
ll have to look). Thanks, Simon On Apr 17, 2010, at 6:34 AM, baptiste auguie wrote: > Dear all, > > I am puzzled by the following behavior of the new grid.cap() function, > which appears to run out of time when capturing the output of a > graphic. It works fine if I introduce a S

Re: [Rd] grid.cap() requires more time?

2010-04-17 Thread Simon Urbanek
On Apr 17, 2010, at 2:43 PM, baptiste auguie wrote: > Hi, > > On 17 April 2010 18:51, Simon Urbanek wrote: >> Baptiste, >> >> first, there is a mailing list specifically for Mac questions - R-SIG-Mac. >> > > I wasn't sure if it was Mac-specific

Re: [Rd] transient memory allocation and external pointers

2010-04-19 Thread Simon Urbanek
n arbitrary memory location which does not necessarily have that semantics. So you can decide to run with it but the fact that this is undocumented means it is not guaranteed to stay that way forever so you may need to change your code if it does. Cheers, Simon > Does anyone know, can I count

Re: [Rd] CRAN: MacOS X binary: not available, see check log?

2010-04-20 Thread Simon Urbanek
On Apr 20, 2010, at 2:57 AM, Henrik Bengtsson wrote: > Hi, > > On Thu, Apr 15, 2010 at 3:45 PM, Simon Urbanek > wrote: >> >> On Apr 15, 2010, at 2:26 AM, Henrik Bengtsson wrote: >> >>> For a couple of days, MacOS X binaries are not build on CRAN (for

Re: [Rd] transient memory allocation and external pointers

2010-04-20 Thread Simon Urbanek
On Apr 19, 2010, at 1:22 PM, Seth Falcon wrote: > On 4/19/10 8:59 AM, Simon Urbanek wrote: >> >> On Apr 19, 2010, at 10:39 AM, Melissa Jane Hubisz wrote: >> >>> Hello, >>> The Writing R extensions manual section 6.1.1 describes the transient >>>

Re: [Rd] transient memory allocation and external pointers

2010-04-20 Thread Simon Urbanek
On Apr 20, 2010, at 10:12 AM, Simon Urbanek wrote: > > On Apr 19, 2010, at 1:22 PM, Seth Falcon wrote: > >> On 4/19/10 8:59 AM, Simon Urbanek wrote: >>> >>> On Apr 19, 2010, at 10:39 AM, Melissa Jane Hubisz wrote: >>> >>>> Hello, >&g

Re: [Rd] Serial connections?

2010-04-20 Thread Simon Urbanek
allowing you to share form Arduino output with several computers or even send remote commands to your Arduino including encryption etc ...). Cheers, Simon PS: From experience I can say that Arduinos are highly addictive so beware ;). > In base::connections documentation, it's not clear

Re: [Rd] Serial connections?

2010-04-20 Thread Simon Urbanek
On Apr 20, 2010, at 11:51 AM, shotwelm wrote: > I've done some microcontroller work over serial also. Unfortunately, > interfacing with a serial port is system dependent, and the mechanisms can be > quite different, as you probably know. It appears that Simon has a solution >

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