Re: [Rd] R.app (PR#7926)

2005-06-10 Thread Simon Urbanek
On Jun 10, 2005, at 11:03 AM, [EMAIL PROTECTED] wrote: > R terminal in aqua interface exits with > > 2005-06-10 16:51:03.826 R[1464] *** -[NSCFType characterAtIndex:]: > selector not > recognized > 2005-06-10 16:51:03.827 R[1464] *** NSTimer discarding exception > 'NSInvalidArgumentException' (r

Re: [Rd] R.app editor (PR#7928)

2005-06-10 Thread Simon Urbanek
You didn't use appropriate subject, didn't provide a reproducible example, didn't read the documentation and the problems you describe are most probably just user errors. (Hint: ever heard of dev.off()?) Please stop spamming the bug report system, and read the posting guide! Thanks, Simon On

Re: [Rd] by should use match.fun

2005-06-12 Thread Simon Urbanek
On Jun 12, 2005, at 3:21 PM, Gabor Grothendieck wrote: > On 6/12/05, Liaw, Andy <[EMAIL PROTECTED]> wrote: > >> I don't get the point. ?by says: >> > > The point is that all other functions of this sort including apply, > sapply, > tapply, lapply work like that so 'by' ought to as well. > > Her

Re: [Rd] R 2.1.1 slated for June 20

2005-06-14 Thread Simon Urbanek
On Jun 14, 2005, at 6:16 PM, Marc Schwartz wrote: > Interesting. Did you do anything different on the ./configure line? > > $ ls -l /usr/bin/f95 > lrwxrwxrwx 1 root root 8 Jun 13 21:18 /usr/bin/f95 -> gfortran > > I just tried it again (having installed some FC updates) and I > still get g77..

Re: [Rd] 2.1.0a for Macs (PR#7952)

2005-06-16 Thread Simon Urbanek
On Jun 16, 2005, at 5:30 PM, [EMAIL PROTECTED] wrote: > I installed the program about a week ago and immediately I started > getting a warning messages particularly when browsing my files > using ls(), search(), gc(), This was fixed in R.app build 1564 and was mentioned several times on the

Re: [Rd] R worked once, now will not open. Works in console, but won't graph. (PR#7953)

2005-06-16 Thread Simon Urbanek
Richard, thank you for the report. From the log it seems to be a problem with your preferences. Please delete the file ~/Library/Preferences/org.R- project.R.plist (e.g. type rm ~/Library/Preferences/org.R-project.R.plist in Terminal or simply delete than file using Finder) and let me know i

Re: [Rd] Failed make (PR#7978)

2005-06-29 Thread Simon Urbanek
On Jun 29, 2005, at 1:52 PM, [EMAIL PROTECTED] wrote: > I downloaded R v2.1.1 earlier this morning to compile under Fedora > Core 4. > It compiled without incident, but 'make check' failed. Below is the > relevant > part of its report. Is this a known problem? My guess is that you're using gf

Re: [Rd] How difficult is it to wrap a large C++ library with R?

2005-07-04 Thread Simon Urbanek
On Jul 4, 2005, at 1:01 PM, Bo Peng wrote: > From what I read from R website, it is easy to wrap individual C/C+ > + functions but not C++ classes. There was a couple of posts about this recently: https://stat.ethz.ch/pipermail/r-devel/2005-April/subject.html Look for the posts concerning C++,

Re: [Rd] allocation of large matrix failing

2005-07-12 Thread Simon Urbanek
James, On Jul 12, 2005, at 5:05 PM, James Bullard wrote: > Hello, this is probably something silly which I am doing, but I > cannot understand why this allocation is not happening. I suspect it's something else - the code you sent us works without problems for me: > .C("foo",as.integer(3

Re: [Rd] segfault with grid and null unit (PR#8014)

2005-07-19 Thread Simon Urbanek
On Jul 19, 2005, at 6:39 AM, [EMAIL PROTECTED] wrote: > Sourcing this code causes the R GUI to crash. I've enclosed a > partial backtrace > from the crash below. I can confirm that this crashes both on OS X (current R-devel) and Linux (2.1.1). The detailed stack trace (with debug symbols) fro

Re: [Rd] mac os x crashes with bioconductor microarray code (PR#8013)

2005-07-20 Thread Simon Urbanek
On Jul 19, 2005, at 12:34 AM, [EMAIL PROTECTED] wrote: > R(1763) malloc: *** vm_allocate(size=346857472) failed (error code=3) > R(1763) malloc: *** error: can't allocate region As the error says, you're obviously running out of contiguous wired memory (RAM). > Any ideas? My computer has 2gb o

Re: [Rd] Testing for English locale

2005-08-01 Thread Simon Urbanek
On Aug 1, 2005, at 10:20 AM, John Fox wrote: > Is there a platform-independent way to test whether R is running in > an English locale? I suppose the following should work: Sys.getlocale("LC_CTYPE")=="C" || length(grep("^en",Sys.getlocale ("LC_CTYPE"),TRUE))>0 Basically unix platforms will h

Re: [Rd] call fortran in R

2005-08-04 Thread Simon Urbanek
On Aug 4, 2005, at 1:38 PM, Sébastien Durand wrote: > Ok, I am presently updating my system. > > How do you set > setenv gcc /usr/local/bin/gfortran. That won't help even if you do it in bash - this is wrong! (F77=gfortran is what may help if you want to re-compile R with gcc4). If you

Re: [Rd] extra parentheses cause death of kernel (PR#8094)

2005-08-24 Thread Simon Urbanek
Mickey, On Aug 24, 2005, at 2:31 PM, [EMAIL PROTECTED] wrote: > I try to type quickly, and sometimes I make mistakes that cost me more > than I think they should... It appears that any time I quickly type a > sequence such as: > > quartz() > > I am rewarded with the following text in red: You'r

Re: [Rd] Free-form to fixed-form Fortran

2005-08-26 Thread Simon Urbanek
Aleši, On Aug 26, 2005, at 10:36 AM, Aleš Žiberna wrote: > I have writen some subrutines in Free-form Fortran. I would like to > includ > them in a package, which I would like to build on WinXP. I have all > suggested tools/programs for bulding R packages on Windows (except > latex). > > What

Re: [Rd] RServe initialization problem

2005-08-29 Thread Simon Urbanek
Joel, On Aug 29, 2005, at 5:57 AM, joelarrais wrote: > I want to use the R functionalities in my Java program. I found the > Rserve > that appear to suite my requirements but I'm facing some configuration > problems. > > I' following the web page tutorial > (http://stats.math.uni-augsburg.de/Rs

Re: [Rd] FW: RServe initialization problem

2005-08-29 Thread Simon Urbanek
On Aug 29, 2005, at 6:04 AM, joelarrais wrote: > I want to use the R functionalities in my Java program. I found the > Rserve > that appear to suite my requirements but I'm facing some configuration > problems. > I' following the web page tutorial > (http://stats.math.uni-augsburg.de/Rserve/doc.

Re: [Rd] A question on R memory management in .Fortran() calls under Windows

2005-09-09 Thread Simon Urbanek
Simone, On Sep 9, 2005, at 1:04 PM, Simone Giannerini wrote: > Dear R community, > > I have a question on how R manages memory allocation in .Fortran() > calls under Windows. > In brief, apparently, it is not possible to allocate large matrices > inside a Fortran subroutine I suspect that th

Re: [Rd] A question on R memory management in .Fortran() calls under Windows

2005-09-12 Thread Simon Urbanek
Simone, On Sep 12, 2005, at 4:30 AM, Simone Giannerini wrote: > yes, CVF allocates automatic objects on the stack and apparently > there is no way of changing it. Yes, that's bad news. > By the way, increasing the stack of the fortran process when > linking does not solve the problem In ge

Re: [Rd] NUMERIC_POINTER question

2005-09-13 Thread Simon Urbanek
Eryk, On Sep 13, 2005, at 2:26 PM, nwew wrote: > printf("%f\n",NUMERIC_POINTER(mat)[1]); > [...] > However it prints > 0. > if [EMAIL PROTECTED] are integers ( [EMAIL PROTECTED]<-matrix(1:12,3,4) ). > > Can anyone explain it to me why? > I thought that NUMERIC_POINTER makes it clear that i ex

Re: [Rd] Project suggestion: Interface between R and graphic devices

2005-10-09 Thread Simon Urbanek
Knut, On Oct 9, 2005, at 1:19 PM, Knut Krueger wrote: >> If you prefer SciViews, JGR, R Commander, etc., then you should >> expect >> some delay before R releases and compatible GUI releases. Indeed, one >> must say that R Commander has always been released on time with the >> latest R version,

Re: [Rd] Control R from another program (written in Delphi)

2005-10-17 Thread Simon Urbanek
Rainer, On Oct 17, 2005, at 1:13 PM, Rainer M. Krug wrote: > At the moment I am using the (D)COM interface but as I would like > to run R on a Linux Cluster, thits is not an option any more. > What is the easiest way of copntrolluing R over the network? I > thought about sockets, but I am a

Re: [Rd] Socks under R

2005-10-19 Thread Simon Urbanek
Rainer, On Oct 19, 2005, at 3:29 PM, Rainer M. Krug wrote: > when I use > > con1 <- socketConnection(...) > > in R and want to send text from another application written in > Delphi to R, do I just have to send the text or do I have to > implement more control characters and so on? Sockets

Re: [Rd] typo in browse.pkgs

2005-11-03 Thread Simon Urbanek
Günther, On Nov 3, 2005, at 10:24 AM, G. Sawitzki wrote: > See below. > > gs. > > Error in browse.pkgs("CRAN", "binary") : couldn't find function > "avaliable.packages" You seem to have an old version of the R.app, because the R 2.2.0 release R GUI has a work-around for that problem. Please

Re: [Rd] Alpha and Beta testing of R versions

2005-11-04 Thread Simon Urbanek
On Nov 4, 2005, at 6:58 AM, Prof Brian Ripley wrote: > Martin's point is generally very valid, but in the case of the > 2.2.0 release remarkably few of the bugs found since release were > new in 2.2.0. > One thing we have learnt is that none of the testers seem to look > at HTML help (which

Re: [Rd] Memory allocation (PR#8304)

2005-11-13 Thread Simon Urbanek
Hans, this is not a bug! You're simply running out of memory as the message tells you (allocating ca. 570MB? That's lot...) . You should consider re-phrasing the problem (preferably) or getting more memory and/or using 64-bit version of R where applicable. Cheers, Simon On Nov 13, 2005, at

Re: [Rd] Help finding some code in the R source code

2005-11-13 Thread Simon Urbanek
Greg, On Nov 13, 2005, at 7:03 PM, Greg Evans wrote: > I'm trying to write some Python code to check if a string text > contains a complete R statement. I'm hoping someone will be able > to point me to the right place in the R source code, so I can use > it as a starting point. What happe

Re: [Rd] external pointers

2005-12-11 Thread Simon Urbanek
Mark, On Dec 12, 2005, at 7:48 AM, <[EMAIL PROTECTED]> wrote: > (i)The first '.C' call uses Delphi code to allocate (using Delphi's > own memory manager) and set up a persistent object that R doesn't > know about. The Delphi code then returns an "opaque" integer-valued > handle to R, which

Re: [Rd] AppleScript commands don't execute until mouse over console window (PR#8405)

2005-12-16 Thread Simon Urbanek
Thanks, Jonathan! I have now committed a slight variation of your patch in the current Mac-GUI. Cheers, Simon On Dec 16, 2005, at 7:30 AM, [EMAIL PROTECTED] wrote: > I am sending commands to R via AppleScript (specifically, from > SubEthaEdit to instruct it to source the file I'm currently

Re: [Rd] Build error on Mac OS X

2005-12-21 Thread Simon Urbanek
Hervé, On Dec 21, 2005, at 6:12 PM, Herve Pages wrote: > I don't get that problem with R-devel daily snapshots from before > 2005-12-14 > and I get it with (almost) all snaphots between 2005-12-14 and today. Strange - I have only failure on 2005/12/17 - all others built fine (same system: 7.

Re: [Rd] cairo anyone?

2005-12-23 Thread Simon Urbanek
Byron, On Dec 22, 2005, at 8:07 PM, Byron Ellis wrote: > Has anyone taken a shot at a Cairo graphics device yet? *opens a drawer* You can try this: http://www.rosuda.org/R/Cairo_0.1-1.tar.gz I'm using it for generating bitmap files (PNG), that's why only the image-backned is used. It should b

Re: [Rd] Rserve setSEXP command

2005-12-26 Thread Simon Urbanek
Hi Chris, On Dec 26, 2005, at 5:57 AM, Chris Burke wrote: > Can any valid SEXP expression be given in the setSEXP command? > > I tried to send a numeric matrix by including the dim attribute > with the data, but get an error code 68 (some parameters are > invalid). Is the dim attribute not su

Re: [Rd] Q: R 2.2.1: Memory Management Issues?

2006-01-05 Thread Simon Urbanek
Karen, On Jan 5, 2006, at 5:18 PM, <[EMAIL PROTECTED]> <[EMAIL PROTECTED]> wrote: > I am trying to run a R script which makes use of the MCLUST package. > The script can successfully read in the approximately 17000 data > points ok, but then throws an error: >

Re: [Rd] Q: R 2.2.1: Memory Management Issues?

2006-01-05 Thread Simon Urbanek
On Jan 5, 2006, at 7:33 PM, <[EMAIL PROTECTED]> <[EMAIL PROTECTED]> wrote: > The empirically derived limit on my machine (under R 1.9.1) was > approximately 7500 data points. > I have been able to successfully run the script that uses package > MCLUST on several hundred smaller data sets. >

Re: [Rd] minor build problem

2006-01-07 Thread Simon Urbanek
Cyrus, thanks for the report. On Jan 7, 2006, at 1:41 PM, Cyrus Harmon wrote: > I'm trying to build from the latest SVN sources on Mac OS X 10.4.3 > and I seem to be having a problem making the documentation. > > When I do make install, i get the following: > > ([EMAIL PROTECTED]):~/src/R/r-deve

Re: [Rd] prod(numeric(0)) surprise

2006-01-09 Thread Simon Urbanek
On Jan 9, 2006, at 3:35 PM, Kjetil Halvorsen wrote: > But this thread seems to have pointed to some inconsistencies: > >> cumprod( numeric(0) ) > numeric(0) >> cumsum( numeric(0) ) > numeric(0) > > shouldn't this give the same as prod() and sum() in this case? No - as Thomas explained very nicely

Re: [Rd] Interfacing with user in R

2006-01-10 Thread Simon Urbanek
On Jan 10, 2006, at 4:34 PM, <[EMAIL PROTECTED]> <[EMAIL PROTECTED]> wrote: > I am new in R programming (my question may sound trivial to you): > is there any way to ask the user to enter a string within an R > process, say a filename, make R to recognise it and open the given > file? Sur

Re: [Rd] Provide both shlib and standard versions of R?

2006-01-15 Thread Simon Urbanek
On Jan 15, 2006, at 11:21 PM, Bo Peng wrote: > To operate R from python via a Python package rpy, R has to be > compiled with --enable-R-shlib. This is troublesome since none of > the binary distributions (except for windows?) is built with this > option That is not true, almost all bina

Re: [Rd] saving PDF with multiple diagrams results in crash (PR#8569)

2006-02-06 Thread Simon Urbanek
On Feb 6, 2006, at 1:11 PM, [EMAIL PROTECTED] wrote: > Full_Name: Alexander Holzbach > Version: 2.2.0 > OS: Mac OS X 10.3.9 > Submission from: (NULL) (129.13.186.1) > > > when i build an area with multiple diagrams (par(mfrow=c(1,3)) ) > and try to save > this to a pdf via "save as.." or by s

Re: [Rd] invalid graphics state using dev.print

2006-02-06 Thread Simon Urbanek
Paul, On Feb 6, 2006, at 5:24 PM, Paul Roebuck wrote: > Tried on R-Sig-Mac with no responses, but I need some kind of answer. > [...] > Does the following work on your system? Interesting, no, it doesn't either. For png and pdf I use Quartz + quartz.save (it produces much nicer results) so I d

Re: [Rd] bugzilla issues

2018-01-26 Thread Simon Urbanek
Thanks, fixed. Simon > On Jan 26, 2018, at 3:40 AM, Uwe Ligges > wrote: > > Simon, > > can you take a look, please? > > Best, > Uwe > > > > On 26.01.2018 01:41, Ben Bolker wrote: >> tl;dr is the R bug tracker down or am I being an idiot? Help please ... >> >> I decided I would foll

Re: [Rd] CRAN indices out of whack (for at least macOS)

2018-01-31 Thread Simon Urbanek
Dirk, yes, thanks, the edge server that serves the Mac binaries to CRAN has run out of disk space (due to size of CRAN itself) so the sync was incomplete. It is fixed now -- you can try by using the macos master server as mirror: https://r.research.att.com/ and it will propagate through other mi

Re: [Rd] readLines function with R >= 3.5.0

2018-05-29 Thread Simon Urbanek
The MySQL DB on the server died - not sure why. Restarted and it should be ok. > On May 29, 2018, at 9:17 AM, Martin Maechler > wrote: > >> Ralf Stubner >>on Tue, 29 May 2018 11:21:28 +0200 writes: > >> On 28.05.2018 16:38, Martin Maechler wrote: >>> Then, I now do think this nee

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 Unavailable from bugzilla currently (

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 fans

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

2019-03-29 Thread Simon Urbanek
Jim, I think the main point of Tomas' post was to alert R users to the fact that there are very serious issues that you have to understand when interfacing R from C++. Using C++ code from R is fine, in many cases you only want to access R data, use some library or compute in C++ and return resu

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
I fully agree with Kevin. Front-ends can always use pthread_atfork() to close descriptors and suspend threads in children. Anyone who thinks you can use PSOCK clusters has obviously not used mclappy() in real applications - trying to save the workspace and restore it in 20 new processes is not

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

2019-04-13 Thread Simon Urbanek
Sure, but that a completely bogus argument because in that case it would fail even more spectacularly with any other method like PSOCK because you would *have to* allocate n times as much memory so unlike mclapply it is guaranteed to fail. With mclapply it is simply much more efficient as it wil

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
Interrupts are not synchronous in R - the signal only flags the request for interruption. Nothing actually happens until R_CheckUserInterrupt() is called at an interruptible point. In you case your code is apparently not calling R_CheckUserInterrupt() until later as a side-effect of the next eva

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

2019-04-30 Thread Simon Urbanek
ve process such a SIGINT is just swallowed, > with a newline outputted to the terminal. > > But apparently, for this background process, it is not swallowed, and > it is triggered later. FWIW it does not happen on Windows, not very > surprisingly. > > Gabor >

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

2019-05-01 Thread Simon Urbanek
pid of the R process, so we can >>> send a SIGINT: >>> >>> Terminal 3: >>> kill -INT pid >>> >>> The R process is of course still running happily. >>> >>> Terminal 2 again: >>> tryCatch(Sys.sleep(10), interrupt = functio

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
Stepan, Andreas gave a lot more thought into what you question in your reply. His question was how you can avoid what you where proposing and have proper threading under safe conditions. Having dealt with this before, I think Andreas' write up is pretty much the most complete analysis I have se

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 mc_exit > needs to wri

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
No, that will make it even worse since you'll be declaring a lot more memory that you actually have. The real problem is that you're ignoring the truncation, so you probably want to use something like if (snprintf(tempname, sizeof(tempname), "%s.%d", of1name, j) >= sizeof(tempname)) Rf_error("

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 Ooms wrote: > >

Re: [Rd] R C API resize matrix

2019-06-17 Thread Simon Urbanek
Matrix is just a vector with the dim attribute. Assuming it is not referenced by anyone, you can set any values to the dim attribute. As for the vector, you can use SET_LENGTH() to shorten it - but I'm not sure how official it is - it was originally designed to work, but there were abuses of TRU

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: > > Thank you Luk

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

2019-12-13 Thread Simon Urbanek
User home is not used by R directly, so it is really up to whatever package/code may be using user home. In our setup we have all machines using NFS mounted homes for years. From experience the only thing to watch for are packages that use their own cache directories in $HOME instead of tempdir(

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

2019-12-14 Thread Simon Urbanek
Laurent, the main point here is that ParseVector() just like any other R API has to be called in a correct context since it can raise errors so the issue was that your C code has a bug of not setting R correctly (my guess would be your'e not creating the initial context necessary in embedded R)

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

2019-12-14 Thread Simon Urbanek
JMP. If you don't use either then you have to use one of the advanced R APIs that do it such as R_ToplevelExec() or R_UnwindProtect(), otherwise your point to abort to on error doesn't exist. Embedding R is much more complex than many think ... Cheers, Simon > Best, > > Lau

Re: [Rd] Downsized R configuration for flat deployment

2019-12-22 Thread Simon Urbanek
DM, can you clarify somewhat what you are exactly concerned about? The standard build of R on Linux is relocatable without any special flags needed since R doesn't use absolute paths but manages library path to its components itself so it's very flexible (e.g., I use this feature to run R jobs

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

2020-01-10 Thread Simon Urbanek
If I understand the thread correctly this is an RStudio issue and I would suggest that the developers consider using pthread_atfork() so RStudio can handle forking as they deem fit (bail out with an error or make RStudio work). Note that in principle the functionality requested here can be easi

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

2020-01-10 Thread Simon Urbanek
ream package developers, the > quickest workaround would be disable forking. If you're conservative, > you could even disable it all of your R processing. Being able to > quickly disable forking will also provide a mechanism for quickly > testing the hypothesis that forking is the unde

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
Jiefei, you did not commit all files into the example package - your example has things like RcppExports.cpp as well as additional flags which are not in your GH project. I suspect the issue is with the extra flags you're adding - those don't come from R. Please make sure you can replicate the

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!\n", p) > flush(p) > readLines(i, 1) [1] "oops!" Cheers, Simon > On 14/0

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
Winston, the Mac CRAN build builds a package only if either is true: 1) the package has not passed checks 2) there is a new version of the package since last successful build+check The old build machine doesn't have the capacity to do full re-builds (it would take over 24h - currently the nightl

Re: [Rd] status of Java & rJava?

2020-03-28 Thread Simon Urbanek
and I can't get rJava 0.9-12 to install -- > and my Ecfun package uses it: I can't get "R CMD build Ecfun" to work on my > Mac nor "R CMD check Ecfun_0.2-4" under Windows. Travis CI builds > "https://github.com/sbgraves237/Ecfun"; just fine. >

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

2020-03-28 Thread Simon Urbanek
ckages' > Warning message: > In install.packages(update[instlib == l, "Package"], l, repos = repos, : > installation of package 'rJava' had non-zero exit status > > > sessionInfo() > R version 3.6.3 (2020-02-29) > Platform: x86_64-w64-mingw32/x64

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

2020-04-16 Thread Simon Urbanek
Serguei, > On 17/04/2020, at 2:24 AM, Sokol Serguei wrote: > > Hi, > > I would like to make a suggestion for a small syntactic modification of FUN > argument in the family of functions [lsv]apply(). The idea is to allow > one-liner expressions without typing "function(item) {...}" to surroun

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

2020-04-16 Thread Simon Urbanek
e clearer some of your point > for me (and may be for others). > > Le 16/04/2020 à 16:48, Simon Urbanek a écrit : >> Serguei, >>> On 17/04/2020, at 2:24 AM, Sokol Serguei wrote: >>> Hi, I would like to make a suggestion for a small syntactic modification of

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

2020-04-21 Thread Simon Urbanek
Tim, as a security precaution Apple has disabled the ability to debug notarized applications*. It means any software distributed on macOS Catalina (and they may have retro-actively enabled it for recent updates of Mojave) cannot be run in a debugger. If you want to debug R, you have to use non

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

2020-04-21 Thread Simon Urbanek
to debug in > that case. > > THK > > On Tue, Apr 21, 2020 at 6:51 PM Simon Urbanek > wrote: > Tim, > > as a security precaution Apple has disabled the ability to debug notarized > applications*. It means any software distributed on macOS Catalina (and they >

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 using mclapply, it fa

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

2020-04-28 Thread Simon Urbanek
] https://github.com/rstudio/rstudio/issues/2597#issuecomment-482187011 >> [1] https://stat.ethz.ch/pipermail/r-devel/2020-January/078896.html >> >> /Henrik >> >> On Tue, Apr 28, 2020 at 2:39 AM Shian Su wrote: >>> >>> Yes I am running on Rstudio 1.2.5033. I

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
Spencer, you shouldn't have anything on the PATH, the location of Java is taken from the registry so you only need t have a valid installation of Java. Better don't set PATH or JAVA_HOME as it will stop rJava from working if you get it wrong. The errors on Windows are confusing, the actual erro

Re: [Rd] defining r audio connections

2020-05-07 Thread Simon Urbanek
The custom connections API was specifically introduced to allow packages to create custom connections back in 2013. Its sole purpose is to allow package authors to create new connections outside of base R, so I don't see why packages using it shouldn't be allowed on CRAN. However, it is solely a

Re: [Rd] GCC warning

2020-05-22 Thread Simon Urbanek
Adrian, newer compilers are better at finding bugs - you may want to read the full trace of the error, it tells you that you likely have a memory overflow when using strncpy() in your package. You should check whether it is right. Unfortunately we can’t help you more specifically, because I don

Re: [Rd] C Interface

2010-06-18 Thread Simon Urbanek
On Jun 18, 2010, at 10:23 AM, michael meyer wrote: > Greetings, > > I am trying to call simple C-code from R. > I am on Windows XP with RTools installed. > > The C-function is > > #include > #include > #include > #include > > // prevent name mangling > extern "C" { > > SEXP __cdecl test

Re: [Rd] How to debug: Cons memory exhausted

2010-06-24 Thread Simon Urbanek
On Jun 20, 2010, at 11:15 AM, Saptarshi Guha wrote: > Hello, > I get an error when binary structures from a pipe > > 'Error: cons memory exhausted (limit reached?)' (but R does not crash) > > This is probably due to some bug in my code, but occurs after reading > about 85K pairs of RAWSXP objec

Re: [Rd] accessing underlying code

2010-07-06 Thread Simon Urbanek
On Jul 6, 2010, at 11:04 AM, Hodgess, Erin wrote: > Dear R Developers: > > Is there a way to look at the underlying code from such items as > R_setup_starma, please? > Yes, of course, they are in the R sources (src/library/stats/src/pacf.c) - that's the beauty of open source. Cheers, Simon

Re: [Rd] Strange R object

2010-07-09 Thread Simon Urbanek
On Jul 9, 2010, at 12:41 PM, Deepayan Sarkar wrote: > On Fri, Jul 9, 2010 at 5:25 AM, Peter Dalgaard wrote: >> Gabor Grothendieck wrote: >>> On Fri, Jul 9, 2010 at 5:09 AM, Peter Dalgaard wrote: Gabor Grothendieck wrote: > I have *** attached *** an RData file containing an R object th

Re: [Rd] R-2.11.1 build and 'so' libraries withouth the 'lib' prefix

2010-07-12 Thread Simon Urbanek
On Jul 12, 2010, at 5:29 AM, lI wrote: > Greetings, > > I have a computer with the following setup: > 1)cblfs (pure 64-bit (amd64) linux), kernel2.6.34 gcc4.4.2 > 2)R-2.11.1 > > I compiled R with BLAS and lapack using the switched ( --with-blas="- > lpthread -latlas -lfptf77blas" > --w

Re: [Rd] R-2.11.1 build and 'so' libraries withouth the 'lib' prefix//update

2010-07-12 Thread Simon Urbanek
On Jul 12, 2010, at 2:50 PM, lI wrote: > On Monday 12 July 2010 11:07:23 lI wrote: >> On Monday 12 July 2010 10:29:30 lI wrote: >>> Greetings, >>> >>> I have a computer with the following setup: >>> 1)cblfs (pure 64-bit (amd64) linux), kernel2.6.34 gcc4.4.2 >>> 2)R-2.11.1 >>> >>> I compiled R w

Re: [Rd] R-2.11.1 build and 'so' libraries withouth the 'lib' prefix//update

2010-07-12 Thread Simon Urbanek
On Jul 12, 2010, at 5:59 PM, lI wrote: > On Monday 12 July 2010 20:52:15 Simon Urbanek wrote: >> On Jul 12, 2010, at 2:50 PM, lI wrote: >>> On Monday 12 July 2010 11:07:23 lI wrote: >>>> On Monday 12 July 2010 10:29:30 lI wrote: >>>>> Greetings, >

Re: [Rd] Precompiled vignette on CRAN

2010-07-14 Thread Simon Urbanek
On Jul 14, 2010, at 4:04 PM, Prof Brian Ripley wrote: > On Wed, 14 Jul 2010, Felix Schönbrodt wrote: > >> Hello, >> >> my package passes R CMD check without any warnings on my local machine (Mac >> OS), as well as on Uwe Ligges' Winbuilder. On RForge, however, we sometimes >> run into problems

[Rd] bug in identical()? [Was: [R-sig-ME] Failure to load lme4 on Mac]

2010-07-17 Thread Simon Urbanek
Daniel, thanks for the test case. I did run it in valgrind but nothing showed up, however ... I'm starting to have a suspicion that this has something to do with identical() - look at this: > identical(M1,M2) [1] FALSE > all(serialize(M1,NULL)==serialize(M2,NULL)) [1] TRUE > identical(unseria

Re: [Rd] bug in identical()? [Was: [R-sig-ME] Failure to load lme4 on Mac]

2010-07-17 Thread Simon Urbanek
s not shown up on other platforms as that is a global issue... (I hope this is the full story - I didn't try all the combinations to see if setting @env to the same environment will appease identical() for all the models) Cheers, Simon On Jul 17, 2010, at 3:49 PM, Simon Urbanek wrote: > D

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