Re: [Rd] R process killed when allocating too large matrix (Mac OS X)

2016-05-04 Thread Simon Urbanek
cted an error that a vector of this size could not be allocated. > > Besides the above (a bug?), how can I find out beforehand whether or > not a square matrix can be allocated? > Can you elaborate on "leads to R being killed"? You should tell to the killer not to

Re: [Rd] R process killed when allocating too large matrix (Mac OS X)

2016-05-04 Thread Simon Urbanek
On May 4, 2016, at 6:14 PM, Marius Hofert wrote: >> Can you elaborate on "leads to R being killed"? You should tell to the >> killer not to do it again :). > > Hi Simon! > > Sure, but who do you tell it if you don't know the killer? > This is all the

Re: [Rd] R process killed when allocating too large matrix (Mac OS X)

2016-05-04 Thread Simon Urbanek
On May 4, 2016, at 9:00 PM, Marius Hofert wrote: > Hi Simon, > > thanks for your quick reply. > > 1) ... so you can reproduce this? Yes, I can on 10.11.4. > 2) Do you know a way how this can be 'foreseen'? We allocate larger > matrices in the copula packag

Re: [Rd] R process killed when allocating too large matrix (Mac OS X)

2016-05-04 Thread Simon Urbanek
all correctly in my case the kill happened in copyVector() -> duplicate(), so it was not necessarily on the initial allocation but rather further down the line. Cheers, Simon > H. > > On 05/04/2016 06:21 PM, Simon Urbanek wrote: >> >> On May 4, 2016, at 9:00 PM, Marius H

Re: [Rd] Single-threaded aspect

2016-05-12 Thread Simon Urbanek
PI calls, but a main one. Other issues involve error handling (you may long-jump out of your thread stack) and global state (devices, connections etc.). In short, it's not something that can be really solved without complete re-design and re-write. Cheers, Simon > On May 12, 2016,

Re: [Rd] R external pointer and GPU memory leak problem

2016-05-16 Thread Simon Urbanek
allocations fail. Cheers, Simon On May 14, 2016, at 11:43 AM, Yuan Li wrote: > My question is based on a project I have partially done, but there is still > something I'm not clear. > > My goal is to create a R package contains GPU functions (some are from > Nividia cuda

Re: [Rd] R without graphics

2016-05-23 Thread Simon Urbanek
Um... any reason why you don't simply disable aqua? That file is only compiled if you enable aqua - it has really nothing to do with grDevices ... On May 23, 2016, at 7:44 PM, Mick Jordan wrote: > Is it possible to configure and build an R without any graphics support. I..e > no grDevices or g

Re: [Rd] String encoding problem

2016-07-07 Thread Simon Urbanek
sn't quite work. To illustrate, doing this in C locale yields a different result: > x [1] "" > y <- iconv(x, from="UTF-8", to = "Shift-JIS") > y [1] "\202\261\202\361\202\311\202\277\202\315" If you wa

Re: [Rd] mcparallel / mccollect

2016-08-30 Thread Simon Urbanek
Michel, thanks, you're right, that the list should have names. Your patch has the match() part backwards, but is otherwise the right idea. I have committed a variant in R-devel and will back-port later. Thanks, Simon > On Aug 30, 2016, at 8:43 AM, Michel Lang wrote: >

Re: [Rd] Web site for MacOSX R-devel precompiled version

2016-09-29 Thread Simon Urbanek
pkg -rw-r--r-- 1 urbanek admin 77935686 Sep 28 23:32 R-devel-mavericks.pkg but it seems that there is a problem with signing the package. I'll look into it. Cheers, Simon > > Thanks, > > Marc > > __ > R-devel@r-project.org ma

Re: [Rd] Web site for MacOSX R-devel precompiled version

2016-09-29 Thread Simon Urbanek
[Moving to R-SIG-Mac where it belongs] The machine building 10.6 binaries has died and since it was responsible for merging the 10.9 and 10.6 binaries to the website it means neither were published. 10.9 binaries are now up. > On Sep 29, 2016, at 2:09 PM, Simon Urbanek > wrote: >

Re: [Rd] Cluster: Various GCC, how important is consistency?

2016-10-17 Thread Simon Urbanek
to be compatible enough. Cheers, Simon > On Oct 17, 2016, at 7:44 PM, Paul Johnson wrote: > > On a cluster that is based on RedHat 6.2, we are updating to R-3.3.1. > I have, from time to time, run into problems with various R packages > and some older versions of GCC. I wish we ha

Re: [Rd] Parallel compression support for saving to rds/rdata files?

2016-12-15 Thread Simon Urbanek
2", "wb") save(mydata, file = con) close(con) load("fname.bz2") you can also use parallel read: load(pipe("pbzip2 -dc fname.bz2")) Cheers, Simon > Second question: Is it possible to make this dummy friendly by allowing > "pigz" as an o

Re: [Rd] Definition of uintptr_t in Rinterface.h

2016-12-29 Thread Simon Urbanek
The problem is elsewhere - Rinterface.h guards the ultima-ratio fallback with HAVE_UINTPTR_T but that config flag is not exported in Rconfig.h. Should be now fixed in R-devel - please check if that works for you. Thanks, Simon > On Dec 26, 2016, at 11:25 PM, Laurent Gautier wrote: >

Re: [Rd] Definition of uintptr_t in Rinterface.h

2017-01-01 Thread Simon Urbanek
> On Jan 1, 2017, at 5:12 PM, Laurent Gautier wrote: > > > > 2017-01-01 8:28 GMT-05:00 Prof Brian Ripley : > On 29/12/2016 15:55, Simon Urbanek wrote: > The problem is elsewhere - Rinterface.h guards the ultima-ratio fallback with > HAVE_UINTPTR_T but that config

Re: [Rd] R Bugzilla down

2017-02-02 Thread Simon Urbanek
Thanks, should be back up. Simon > On Feb 2, 2017, at 6:38 AM, Mikko Korpela wrote: > > The R Bugzilla at <https://bugs.r-project.org/bugzilla3/> is down, for at > least some hours by now. > > The error message from my web browser reads: > > Can't conn

Re: [Rd] R 3.4 and mclapply assertion failure - is this a bug?

2017-05-02 Thread Simon Urbanek
Yan, this looks like an interaction of OpenMP in data.table and forking - you may want to report that to Matt as he can shed more light on that. He has been complaining that we didn't enable OpenMP before 3.4 so he probably knows about the issue and how to fix it. Cheers, Simon >

Re: [Rd] lm() gives different results to lm.ridge() and SPSS

2017-05-04 Thread Simon Bonner
that helps. Cheers, Simon ## Load packages library(MASS) ## Set seed set.seed() ## Set parameters n <- 100 beta <- c(1,0,1) sigma <- .5 rho <- .75 ## Simulate correlated covariates Sigma <- matrix(c(1,rho,rho,1),ncol=2) X <- mvrnorm(n,c(0,0),Sigma=Sigma) ## Simulate data mu &

Re: [Rd] Custom connections

2017-06-12 Thread Simon Urbanek
ely intended to be used by packages so it's ok to use it on CRAN. Although I cannot speak for the author, I suspect this change merely helps to flag where the API is used to follow the trail of breakage in R-devel. Cheers, Simon > Thank you, > Gabor > > ___

Re: [Rd] [WISH / PATCH] possibility to split string literals across multiple lines

2017-06-14 Thread Simon Urbanek
I can think of with multiline strings do that as that's way too dangerous. Cheers, Simon > On Jun 14, 2017, at 6:58 AM, Andreas Kersting wrote: > > Hi, > > I would really like to have a way to split long string literals across > multiple lines in R. > > Cu

Re: [Rd] Wrongly converging glm()

2017-07-20 Thread Simon Bonner
s in the C implementation then the other convergence criterion will be satisfied and the code will say that the algorithm has converged. In the end, it's up to the analyst to be aware of the pitfalls and how to address them. Cheers, Simon > -Original Message- > From: R-devel [mai

Re: [Rd] Help to create bugzilla account

2017-08-12 Thread Simon Urbanek
will have another object on top so in most practical cases malloc.trim() doesn't actually do anything. You can always call malloc.trim() yourself is you think it helps, but it doesn't in the general case. The only way to address that would be to move allocated objects from top of the po

Re: [Rd] Help to create bugzilla account

2017-08-13 Thread Simon Urbanek
; nusance of having to add configure checks. It would also be necessary > to make sure that adding this doesn't significantly ompact malloc > performance. > > I don't know if this issue exists on Windows as well; it might as the > basic malloc we use there is the same as used

[Rd] side-effect of calling functions via `::`

2017-09-01 Thread Simon Barthelmé
one. In my case it led to a bug that was rather hard to track down because it looked like non-deterministic behaviour. Shouldn't there at least be a warning about such side effects, the way library() tells you about masking? Best Simon Barthelme _

Re: [Rd] side-effect of calling functions via `::`

2017-09-01 Thread Simon Urbanek
le to fix that so in principle it shouldn't make a difference performance wise. Cheers, Simon > On Sep 1, 2017, at 8:03 AM, Martin Maechler > wrote: > >>>>>> Lionel Henry >>>>>> on Fri, 1 Sep 2017 13:47:07 +0200 writes: > >> A packa

Re: [Rd] side-effect of calling functions via `::`

2017-09-01 Thread Simon Urbanek
le to fix that so in principle it shouldn't make a difference performance wise. Cheers, Simon > On Sep 1, 2017, at 8:03 AM, Martin Maechler > wrote: > >>>>>> Lionel Henry >>>>>>on Fri, 1 Sep 2017 13:47:07 +0200 writes: > >> A p

Re: [Rd] How to create a table structure in Java code?

2017-10-26 Thread Simon Urbanek
You are entering the quoting hell - you are missing quotes and escapes for \n. it would be much more reasonable to use the rConnection.assign method instead of pasting any content through the parser. Cheers, Simon > On Oct 26, 2017, at 9:59 AM, Morkus via R-devel wrote: > > That&

[Rd] Fixed BLAS tests for external BLAS library

2017-12-18 Thread Simon Guest
/usr/lib64/tkConfig.sh \ --enable-R-shlib \ --enable-prebuilt-html cheers, Simon __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

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] 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] 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

[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] 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/

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] 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] ...()

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] 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] 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

2022-09-26 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
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
> 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
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
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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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

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