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

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

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

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

Re: [Rd] Wayland Display Support in R Plot

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

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

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

Re: [Rd] Regenerate news feeds?

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

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

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

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

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

Re: [Rd] Determining the size of a package

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

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

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

Re: [Rd] Advice debugging M1Mac check errors

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

Re: [Rd] Advice debugging M1Mac check errors

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Re: [Rd] R 3.0.1 : parallel collection triggers "long memory not supported yet"

2013-05-31 Thread Simon Urbanek
the transmission so the result for one worker cannot exceed 2Gb. I'll put long vector support on my ToDo list. In your case you should be able to work around it by disabling pre-scheduling (you may want to do some grouping if you have 30,000 short iterations, though). Cheers, Simon _

Re: [Rd] Compile error with gfortran-4.6

2013-06-09 Thread Simon Urbanek
On Jun 9, 2013, at 5:50 PM, Fabio Mathias Corrêa wrote: > Dear prof. Brian Ripley, > > Thanks for help! > > I compiled using the command: > > > MAKEFLAGS="FCFLAGS=-fopenmp" R CMD SHLIB hello.f90 > Obviously, that won't work. Not only are you abusing MAKEFLAGS for something that it's not des

Re: [Rd] dmvnorm

2013-06-10 Thread Simon Urbanek
alone is not sufficient, if you want to use it in threads, you would need a thread-safe version. This means that you really need your own version, so I don't think adding C version of dmvnorm to R has necessarily any bearing to what you are trying to do. Cheers, Simon > + The mvtnorm packa

Re: [Rd] R CMD INSTALL and file permission settings

2013-06-14 Thread Simon Urbanek
of users! Although it's certainly a step up from the previously hard-coded default, I would argue that the most desired behavior is to follow the permissions already set up. If the library is setup to be group-writable then the package should be installed group-writable. The point i

Re: [Rd] R CMD INSTALL and file permission settings

2013-06-14 Thread Simon Urbanek
On Jun 14, 2013, at 4:35 PM, Dirk Eddelbuettel wrote: > > On 14 June 2013 at 16:17, Simon Urbanek wrote: > | I think it would be better to have a bit more sane handling of this. The > decision is rarely at the install time of the package -- e.g. did you adjust > the flag

Re: [Rd] R CMD INSTALL and file permission settings

2013-06-15 Thread Simon Urbanek
On Jun 14, 2013, at 11:27 PM, Dirk Eddelbuettel wrote: > > On 14 June 2013 at 16:56, Simon Urbanek wrote: > | On Jun 14, 2013, at 4:35 PM, Dirk Eddelbuettel wrote: > | > But up until right now I could not update a package a colleague installed, > | > and vice ve

Re: [Rd] R CMD INSTALL and file permission settings

2013-06-15 Thread Simon Urbanek
On Jun 15, 2013, at 2:42 PM, Martin Maechler wrote: >>>>>> Dirk Eddelbuettel >>>>>>on Sat, 15 Jun 2013 10:45:04 -0500 writes: > >> On 15 June 2013 at 07:00, Dirk Eddelbuettel wrote: >> | >> | On 15 June 2013 at 07:47, Simon Urbane

Re: [Rd] How can C++ read the R object written into socket with saveRDS or save

2013-06-26 Thread Simon Urbanek
s the kind of payload and its length, then the serialization follows in the payload. That way you only need to read a fixed header. Cheers, Simon > I do not do any conversion with the received data, and only need to > transfer them into a remote R to do the function execution. > &

Re: [Rd] Read a text file into R with .Call()

2013-06-27 Thread Simon Urbanek
e into a raw vector and use accessor function to create strings on demand - but this is only meaningful when you plan to use a very small subset. Cheers, Simon > I know I cam refer to the Biostrings pakcage's way of readDNAStringSet, but > that is a bit complicated

Re: [Rd] Read a text file into R with .Call()

2013-06-27 Thread Simon Urbanek
uot;\n", x, fixed=TRUE) to get an index of the lines. As I said, the premise here is that you need only a small fraction of the content. If you really need them all as strings, then you have to load them all anyway. Cheers, Simon > I attached more complete code I wrote. PS: Just mino

Re: [Rd] Save R Objects in C Code

2013-06-30 Thread Simon Urbanek
se R_GlobalEnv - it's the closes to what most people need (if you need something else then you know how to get that env ;)). Cheers, Simon > SEXP Save(SEXP X,SEXP File) > { > char Name='X'; > > SEXP EnvList; > PROTECT(EnvList=allocList(1)

Re: [Rd] Ctrl+C in R will terminate the child process which is spawned by using "pipe"

2013-07-02 Thread Simon Urbanek
(fork()) exit) so you disassociate the child from the parent group or to possibly use setsid(), both as to not share the terminal with the parent. Cheers, Simon > 1. I used pipe to spawn one C++ process, which will running in a loop > without exiting immediately. > > z <- pipe(

Re: [Rd] R-devel Digest, Vol 125, Issue 2

2013-07-05 Thread Simon Urbanek
On Jul 4, 2013, at 3:53 AM, gianluca mastrantonio wrote: > I'm just a beginner, so i can make some stupid error. > I use the "-l cov.model.h -l util.h" because i need to load another two c++ > programs (cov.model.cpp and util.cpp) > Well,then you probably meant R CMD SHLIB SpTempWrapC.cpp co

Re: [Rd] Cross-platform linking of a simple front-end

2013-07-05 Thread Simon Urbanek
can correct this by adding "-lm" manually to the command, but I'm not > sure how portable that will itself be. > My guess would be that you did not use --enable-R-shlib when compiling R on Ubuntu so you don't have a shared version of the R library to link against

Re: [Rd] robustbase compilation problem: probably boneheaded? maybe 32-bit?

2013-07-11 Thread Simon Urbanek
CTOR_SUPPORT since the latter is irrelevant here as R 3.0.0+ will have R_xlen_t regardless of the long vector support. Cheers, Simon > robustbase is passing its package checks: > http://cran.r-project.org/web/checks/check_results_robustbase.html > > ... but from the names of the tar

Re: [Rd] unmapped memory core dump with pure R program?

2013-07-14 Thread Simon Urbanek
. That said, R-devel has quite a few new bugfixes, so I'd suggest that you may want to replicate it there first. Cheers, Simon > regards, > > /iaw > > Ivo Welch (ivo.we...@gmail.com) > > > > On Sun, Jul 14, 2013 at 2:54 AM, Dirk Eddelbuettel wrote: >

[Rd] Problem with distributing data in package.

2013-07-19 Thread Simon Knapp
is there another 'R-ish' way to achieve a similar result? Just in case it is useful, I have included the code I use to build the netcdf file and 'ncdf' object below. Thanks in advance, Simon Knapp #--R code starts here-- #

Re: [Rd] Problem with distributing data in package.

2013-07-20 Thread Simon Knapp
windows binary package (.R files) if anyone can tell me. Thanks again, Simon On Sat, Jul 20, 2013 at 4:58 PM, Barry Rowlingson wrote: > On Fri, Jul 19, 2013 at 10:33 AM, Simon Knapp wrote: >> Hi List, >> >> I am building a package for a client to help them create and perform &g

Re: [Rd] Problem with distributing data in package.

2013-07-20 Thread Simon Knapp
--help`, there is no mention of it in R-exts.pdf and my ability to use Google is clearly lacking... though I did try that), but it appears to be exactly what I need - Thankyou! Kind Regar

Re: [Rd] Understanding modification in place

2013-07-24 Thread Simon Urbanek
es. If you just eval it, you'll get the same behavior as in the console: > p=parse("test.R") > eval(p) Global @100816498 13 INTSXP g0c2 [NAM(1)] (len=3, tl=0) 1,2,3 @100816498 13 INTSXP g0c2 [NAM(1)] (len=3, tl=0) 1,1,3 In function @102c42378 13 INTSXP g0c2 [NAM(1)]

Re: [Rd] package compilation on OSX 10.8 -- error compiling Fortran library for architecture i386

2013-07-25 Thread Simon Urbanek
#x27;re using the wrong compiler flags for building the dependent library inside your package (as the message tells you: you are building 64-bit version of libmseed when compiling 32-bit version of the package). Please make sure you use the proper compiler and flags that R is providing (i.e

Re: [Rd] How to best implement package options?

2013-07-26 Thread Simon Urbanek
the wheel". > > > What is considered "best practice" for implementing package options? > Any of the above, or something different? > Personally, I hate when packages use their own option management system because it leads to vastly inconsistent behavior, so I p

Re: [Rd] Adding text comments to graphics device output files?

2013-07-31 Thread Simon Urbanek
On Jul 30, 2013, at 11:04 PM, Duncan Temple Lang wrote: > > Hi Henrik > > I have some extensions of Simon U's png package > to read and write metadata elements for PNG. > They are at > https://github.com/duncantl/png.git > > When I have time to complet

Re: [Rd] Adding text comments to graphics device output files?

2013-07-31 Thread Simon Urbanek
the PNG info, so it is now simply extending that concept. You can store native text key/values pairs. In addition, R-native matadata can be attached -- it is stored as a special key "R.metadata" holding the serialization of the R object. See the last example in http://rforge.net/doc/pac

Re: [Rd] Depends vs Imports

2013-07-31 Thread Simon Urbanek
al purposes, not technically) import a function into a package = make sure that this function works in my package regardless of the search path (so I can write fn1 instead of pkg1::fn1 and still know it will come from pkg1 and not someone's workspace or other package that chose the same name) Cheers, Simon __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Multiple return values / bug in rpart?

2013-08-13 Thread Simon Urbanek
On Aug 13, 2013, at 5:27 AM, Barry Rowlingson wrote: > On Mon, Aug 12, 2013 at 6:06 PM, Justin Talbot wrote: >> In the recommended package rpart (version 4.1-1), the file rpartpl.R >> contains the following line: >> >> return(x = x[!erase], y = y[!erase]) >> >> AFAIK, returning multiple values

Re: [Rd] Inconsistency between eval and withVisible (with patch)

2013-08-15 Thread Simon Urbanek
that this is documented very explicitly: "eval’ evaluates its first argument in the current scope before passing it to the evaluator" whereas withVisible only does the first part: "The argument is evaluated in the caller's context." Cheers, Simon > ~G > > >

Re: [Rd] as.Date.character speed improvement suggestion

2013-08-16 Thread Simon Urbanek
not for any of ours because we are always dealing with timestamps - but that's why we use POSIXct and not Date), but I'd argue that you may as well do it right away in your specialized application instead. Cheers, Simon > I suspect most everyone with large vectors of c

Re: [Rd] How does R_UnboundValue and removing variables work?

2013-08-18 Thread Simon Urbanek
Peter, On Aug 18, 2013, at 9:12 AM, Peter Meilstrup wrote: > Reading "R Internals" made me believe that R_UnboundValue was a placeholder > that would be skipped over in variable lookup. viz. the section of R > Internals "Hash tables" says "items are not actually deleted but have their > value set

Re: [Rd] Makevars and Makeconf sequencing

2013-08-23 Thread Simon Urbanek
On Aug 23, 2013, at 7:53 PM, Ross Boylan wrote: > http://cran.r-project.org/doc/manuals/R-exts.html#Configure-and-cleanup > near the start of 1.2.1 Using Makevars says > >> There are some macros which are set whilst configuring the building of >> R itself and are stored in R_HOME/etcR_ARCH/Make

Re: [Rd] Memory allocation in read.table

2013-08-28 Thread Simon Urbanek
to the data (i.e. NAMED < 2). If there are two references, they have to copy, because it would change the other copy. Here, however, it already has NAMED=2 because of data <- data[keep] If you remove that line and inverse the order of class() and attr()<- then you get 0 copies. Che

Re: [Rd] Memory allocation in read.table

2013-08-28 Thread Simon Urbanek
ow so high that CPUs are the bottlenecks now, not vice versa. Re fast loading - yes, that's something I was also working around in iotools https://github.com/s-u/iotools Cheers, Simon __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Memory allocation in read.table

2013-08-28 Thread Simon Urbanek
r anything else factors - which are integers) so the above works for me just fine. I am working on a way to do direct mmap serialization of SEXPs but it's not ready yet (basic vectors are supported but complex objects not yet). Cheers, Simon _

Re: [Rd] Why does an empty vector occupy 40 bytes?

2013-08-29 Thread Simon Urbanek
On Aug 29, 2013, at 9:39 AM, Hadley Wickham wrote: > Hi all, > > Why is the object size of an empty vector 40 bytes? (At least in 64-bit R.) > > object.size(integer(0)) > # 40 bytes > > Reading R internals, it looks like it should be: > > * 4 bytes: sxpinfo header (= 32 bits) > * 8 bytes: poi

Re: [Rd] Why does an empty vector occupy 40 bytes?

2013-08-29 Thread Simon Urbanek
On Aug 29, 2013, at 12:08 PM, Hadley Wickham wrote: >> You have not: the start of the vector area also needs to be aligned (since >> it might hold doubles or CHARSXPs). > > Thanks, that was the key point I was missing. (Also mentioned to me off list > by Luke Tierney). > Not to be picky, but t

Re: [Rd] Why does an empty vector occupy 40 bytes?

2013-08-29 Thread Simon Urbanek
On Aug 29, 2013, at 2:37 PM, Hadley Wickham wrote: >> Not to be picky, but that is not the point. The alignment is due to the >> attrib pointer which is at offset 8 despite the fact that there is only a >> 4-byte element in front of it. Maybe for better illustration, this is the >> layout on 6

Re: [Rd] Why does an empty vector occupy 40 bytes?

2013-08-29 Thread Simon Urbanek
e; char active; char *description; int len; }; takes 40 bytes on 64-bit machine, while just re-ordering the members to struct b { char *name; char *description; char flag; char active; int len; }; takes 24 bytes. Chee

Re: [Rd] Why does duplicate() make deep copies?

2013-09-05 Thread Simon Urbanek
fforts underway by Luke Tierney and Michael Lawrence to see how far we can go without breaking everything. Cheers, Simon __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

[Rd] Package installation and path.package

2013-09-09 Thread Simon Zehnder
quot;mmstructBASE"), prototype(conn = dbConnect(dbDriver("SQLite"), .defaultDBPath())) ) I understand the error, but I would like to have a workaround. How can I give the path to the package I am actually installing without getting this error? Best Simon __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Package installation and path.package

2013-09-09 Thread Simon Urbanek
On Sep 9, 2013, at 4:22 AM, Simon Zehnder wrote: > Dear R-Devels, > > I am writing right now my own package that makes use of 'tempfile' and there > within with 'path.package'. When I install it, I get the error: Error in > path.package("mypackage"

Re: [Rd] Package installation and path.package

2013-09-09 Thread Simon Urbanek
On Sep 9, 2013, at 9:26 AM, Simon Urbanek wrote: > > On Sep 9, 2013, at 4:22 AM, Simon Zehnder wrote: > >> Dear R-Devels, >> >> I am writing right now my own package that makes use of 'tempfile' and there >> within with 'path.package'.

Re: [Rd] Invalid UTF-8 with gsub(perl=TRUE) and iconv(sub="")

2013-09-09 Thread Simon Urbanek
On Sep 9, 2013, at 12:46 PM, Milan Bouchet-Valat wrote: > Le lundi 09 septembre 2013 à 13:59 +0100, Prof Brian Ripley a écrit : >> On 09/09/2013 09:49, Milan Bouchet-Valat wrote: >>> Hi! >>> >>> I experience an error with an invalid UTF-8 character passed to >>> gsub(..., perl=TRUE); the interest

Re: [Rd] R CMD config for R >= 3.0.1

2013-09-10 Thread Simon Urbanek
irly recently on a CentOS machine, so I know it's possible, but there are a few gotchas that may require a few symlinks created by hand). Cheers, Simon > > -- > View this message in context: > http://r.789695.n4.nabble.com/R-CMD-config-for-R-3-0-1-tp4667399p4675814.html &g

Re: [Rd] [PATCH] show vector length in summary()

2013-09-10 Thread Simon Urbanek
On Sep 10, 2013, at 12:56 PM, Sam Steingold wrote: >> * Dirk Eddelbuettel [2013-09-10 10:21:33 -0500]: >> >> On 10 September 2013 at 10:32, Sam Steingold wrote: >> | (summary.default): show the vector length in addition to quantiles >> | >> | >> | diff -u -i -p -F '^(def' -b -w -B >> /home/s

Re: [Rd] Package installation and path.package

2013-09-10 Thread Simon Zehnder
Hi Simon, thank you for this comment! I will do it now the regular way - this is always the most reliable one. Best Simon On Sep 9, 2013, at 3:29 PM, Simon Urbanek wrote: > e you need something that the user has write-permissions for. __ R-de

Re: [Rd] Package installation and path.package

2013-09-10 Thread Simon Zehnder
Hi Dirk, thanks for the help I take a more thorough look at it. Best Simon On Sep 9, 2013, at 3:41 PM, Dirk Eddelbuettel wrote: > > On 9 September 2013 at 09:26, Simon Urbanek wrote: > | On Sep 9, 2013, at 4:22 AM, Simon Zehnder wrote: > | > I am writing right now my own pac

[Rd] Design for classes with database connection

2013-09-18 Thread Simon Zehnder
crostructure models by calling package-specific functions. Is there a big fault in my design, something I haven't considered? I am very sure on this list are researchers and developers with much more experience. I would like to hear your opinion and ideas. I learn from it and can maybe get to a design which I can then implement for the research on such data and models. Best Simon __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Design for classes with database connection

2013-09-20 Thread Simon Zehnder
as suggested in your >last comment. Best Simon On Sep 20, 2013, at 12:27 AM, Paul Gilbert wrote: > Simon > > Your idea to use SQLite and the nature of some of the sorting and extracting > you are suggesting makes me wonder why you are thinking of R data structures > as

Re: [Rd] regenerate Rscript after moving R installation

2013-09-21 Thread Simon Urbanek
install rhome= where is some path that I can always create a symlink in (I also use DESTDIR so that path doesn't actually need to exist on the build machine and it avoid polluting --prefix which is not needed). That way you can move R wherever you want as long so you keep that one syml

Re: [Rd] regenerate Rscript after moving R installation

2013-09-21 Thread Simon Urbanek
I forgot to mention that some packages bake-in paths as well, so even if you fix both R and Rscript, it will still not work in general. On Sep 22, 2013, at 3:42 AM, Simon Urbanek wrote: > On Sep 21, 2013, at 8:43 PM, Tobias Verbeke > wrote: > >> L.S. >> >> In t

Re: [Rd] Capture output of install.packages (pipe system2)

2013-09-23 Thread Simon Urbanek
estion: there is keep_outputs which allows to re-direct a copy of the output into a file - at least for the actual install part of it. On top of my head for full capture I can only think of custom C code that will re-direct stderr/out FDs as desired (it's really trivial to re-direct to file

Re: [Rd] regenerate Rscript after moving R installation

2013-09-24 Thread Simon Urbanek
Murray, On Sep 24, 2013, at 2:18 AM, Murray Stokely wrote: > Simon, do you have some examples of packages with this attribute? As Brian pointed out, some of them concern linking (I'm typically worried about OS X and Dirk has fixed Rcpp there), but there are also others that store

Re: [Rd] Possible POSIXlt / wday glitch & bugs.r-project.org status

2013-10-05 Thread Simon Urbanek
e official R-project.org DNS is updated (but I have no idea how long that may take). Cheers, Simon > https://stat.ethz.ch/pipermail/r-help/2013-October/360958.html > > Scott > >> >> ``` >> ping bugs.r-project.org >> PING rbugs.research.att.com (207.140.168

Re: [Rd] Allow semantic versioning for packages

2013-10-05 Thread Simon Urbanek
that you are forced to use something meaningful is for a good reason here. Cheers, Simon On Oct 4, 2013, at 8:53 PM, Gábor Csárdi wrote: > Dear R developers, > > (http://bugs.r-project.org/ seems to be down, so I am writing a feature > request here.) > > It would be

Re: [Rd] Possible POSIXlt / wday glitch & bugs.r-project.org status

2013-10-05 Thread Simon Urbanek
may be worked around - and that remains to be investigated. Cheers, Simon > On 5 October 2013 02:37, Joshua Ulrich wrote: >> On Fri, Oct 4, 2013 at 8:02 PM, Imanuel Costigan wrote: >>> Thanks for the responses and quoting the timezone help file. >>> >>> I a

Re: [Rd] Allow semantic versioning for packages

2013-10-05 Thread Simon Urbanek
Gabor, On Oct 5, 2013, at 4:58 PM, Gábor Csárdi wrote: > Simon, > > I think there is a misunderstanding here. I am not suggesting anarchy, > completely the opposite. > > Semantic versioning as defined on http://semver.org was designed exactly for > being able to or

Re: [Rd] Allow semantic versioning for packages

2013-10-07 Thread Simon Urbanek
On Oct 5, 2013, at 9:19 PM, Gábor Csárdi wrote: > On Sat, Oct 5, 2013 at 2:23 PM, Simon Urbanek > wrote: > Gabor, > > On Oct 5, 2013, at 4:58 PM, Gábor Csárdi wrote: > > > Simon, > > > > I think there is a misunderstanding here. I am not suggesting a

Re: [Rd] Allow semantic versioning for packages

2013-10-08 Thread Simon Urbanek
On Oct 7, 2013, at 7:35 PM, Gábor Csárdi wrote: > On Mon, Oct 7, 2013 at 6:32 PM, Simon Urbanek > wrote: > On Oct 5, 2013, at 9:19 PM, Gábor Csárdi wrote: > [...] > e.g. quoting the spec: "Build metadata SHOULD be ignored when determining > version precedence." &

Re: [Rd] Parallel R expression evaluations

2013-10-18 Thread Simon Urbanek
lel. Also you can use the embedded init only once. If you break any of these rules, the behavior is undefined (and everything comes down crashing). Cheers, Simon > I am executing round(X) and abs(X) parallelly on a set of 50 input rows > which resulted in segmentation fault after gett

Re: [Rd] Parallel R expression evaluations

2013-10-20 Thread Simon Urbanek
Jai, On Oct 19, 2013, at 1:37 AM, JaiReddy wrote: > Thanks Simon. > > May I know how R works if two expressions come at the same time for > evaluation. When I debug my case I found that issue was found with indexed > values of protected items. > > As R is single threade

Re: [Rd] Subversion log no longer being updated daily

2013-10-20 Thread Simon Urbanek
with all the server switching I forgot to put some pieces that Duncan was running on the new server. It should be all working now. Thanks, Simon __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] png(type='cairo'): point symbols without boarders are not anti-aliased?

2013-10-22 Thread Simon Urbanek
ist(deldir(rnorm(200),rnorm(200 polygon(p$x,p$y,col=heat.colors(15)[runif(1,1,15)], border=NA) That said, in our experience the Cairo approach works very well in practice. Cheers, Simon > png(): http://i.imgur.com/lKrFG9i.png > CairoPNG(): http://i.imgur.com/Dv0rsKK.png > > f

Re: [Rd] R CMD check problem with R 3.0.2

2013-10-26 Thread Simon Urbanek
e for both INSTALL and check to bail out if not presented with a file -- it would save a lot of people a lot of time spent in chasing ghost issues. Cheers, Simon > Regards, > Yihui > -- > Yihui Xie > Web: http://yihui.name > Department of Statistics, Iowa State University >

Re: [Rd] cat with backspace and newline characters

2013-11-06 Thread Simon Urbanek
icit assumption is that “\b” is interpreted in some way, but it’s not - it’s simply passed on. When running on a terminal, it is interpreted by the terminal, and the standard interpretation is to move the cursor to the left by one character. If running R through any other means like a GUI, it’s

[Rd] R CMD INSTALL - problem with working directory

2013-11-08 Thread Simon Zehnder
o me: system("ls -hFGlxo /Users/simonzehnder/Library/R/R-gcc") total 0 drwxr-xr-x 7 simonzehnder 238B Nov 8 10:37 library/ R CMD INSTALL seems to need a working directory that equals the actual working directory. Is there a workaround, that makes things work for m

Re: [Rd] problem using rJava with parallel::mclapply

2013-11-11 Thread Simon Urbanek
Is this a bug or a limitation of rJava ? It’s a limitation of the Java runtime - you cannot fork a JVM. This is true for most libraries that use long-lived threads or any kind if UI (see the warnings in mcfork). Cheers, Simon > Or is there a good practice for rJava clients to avoid this pr

Re: [Rd] R CMD SHLIB error bad value (core2) for -mtune= switch

2013-11-15 Thread Simon Zehnder
No information has been given, where this error occurred. What were you doing? Simon On 15 Nov 2013, at 10:49, pranav.waila wrote: > I am getting the following error. Please help if the problem is resolved: > > $ make > 0 [main] make 10092 stdio_init: couldn't make std

Re: [Rd] serialization for external pointers

2013-11-16 Thread Simon Urbanek
is still missing it the ability to set a hook to update the save object on save() - since we don’t necessarily want to add the extra information every time the object is created or the serialization may become stale over time. That would still be very useful to add … Cheers, Simon > One way

Re: [Rd] Blank lines in DESCRIPTION

2013-11-26 Thread Simon Urbanek
tolerated, because there is no second paragraph in that case. If you look at the commit you quote (r60495), it specifically adds an error if there is more than one paragraph. Cheers, Simon On Nov 26, 2013, at 6:03 PM, Laurent Gatto wrote: > Dear R-devel list, > > I would like to enquire

Re: [Rd] Checking packages with address sanitizer

2013-11-27 Thread Simon Urbanek
t will automatically work for packages. The above seems like you're trying to use AS just for the package, but that cannot work, because it's missing all the AS runtime libraries which must be in the main executable -- i.e. R. Cheers, Simon > Thanks in advance > Wolfgang &g

Re: [Rd] inflate zlib compressed data using base R or CRAN package?

2013-11-28 Thread Simon Urbanek
explicitly to mean “zlib” so I’m not sure there is a good way out. Cheers, Simon > > On Wed, Nov 27, 2013 at 5:22 PM, Dirk Eddelbuettel wrote: > >> >> On 27 November 2013 at 18:38, Dirk Eddelbuettel wrote: >> | >> | On 27 November 2013 at 23:49, Dr Gregory Je

Re: [Rd] inflate zlib compressed data using base R or CRAN package?

2013-11-29 Thread Simon Urbanek
On Nov 29, 2013, at 4:37 AM, Henrik Bengtsson wrote: > On Thu, Nov 28, 2013 at 4:48 PM, Simon Urbanek > wrote: >> On Nov 27, 2013, at 8:30 PM, Murray Stokely wrote: >> >>> I think none of these examples describe a zlib compressed data block inside >>> a

Re: [Rd] internal manipulation of ...

2013-12-12 Thread Simon Urbanek
... can be evaluated. > Arguments in ... are evaluated *before* being passed down to .Call/.External so there is no ... by the time you enter the C code. AFAIR R doesn't allow you to get at the promises outside of internal code, so you either get the call or the values, but nothing in be

Re: [Rd] Strategies for keeping autogenerated .Rd files out of a Git tree

2013-12-13 Thread Simon Urbanek
There are some talks about providing the above as a cloud service, so that anyone can run and/or use it. Cheers, Simon On Dec 13, 2013, at 8:51 AM, Kirill Müller wrote: > On 12/13/2013 12:50 PM, Romain Francois wrote: >> Pushing back to github is not so difficult. See e.g >>

Re: [Rd] RHS of assignment is evaluated eagerly?

2013-12-26 Thread Simon Urbanek
assignment is right associative i.e. a <- b <- c is parsed as a <- (b <- c). */ Compare to > `test<-`(x, print("evaled arg"), print("evaluated value")) [1] 1 Cheers, Simon __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] reference class internals

2014-01-09 Thread Simon Urbanek
uaranteed to not be touched. Reference-semantics objects in R are literally passed by reference (same C pointer), so yes, it is true pass-by-reference. Cheers, Simon (*) - technically, there is a thin non-refernce wrapper around the instances of reference classes, because there are things you d

Re: [Rd] My first package

2014-01-18 Thread Simon Urbanek
can get latest R-devel builds for Mac OS X from http://r.research.att.com and the same is true for binary packages for R-devel - simply use http://r.research.att.com as the repository (in fact most CRAN mirrors should work as well). Cheers, Simon > 2) Not sure if this one belongs to this list. Does l

Re: [Rd] [R-SIG-Mac] My first package

2014-01-20 Thread Simon Urbanek
d R-devel, and never ever had a problem, had a report of a problem or had > a note from CRAn about my packages not being ok because I built them with > R-relase (or whatever it might be called) and not R-devel. > You got lucky so far ;). See earlier post - you're answering to an

Re: [Rd] String Vector Encoding

2014-02-03 Thread Simon Urbanek
On Feb 3, 2014, at 10:06 AM, Saptarshi Guha wrote: > True but I was hoping someone could point me where in the source code this > happens. > src/main/serialize.c @1655 and @1663 > Cheers > Saptarshi > On Feb 3, 2014 3:37 AM, "Duncan Murdoch" wrote: > >> On 14-02-03 3:41 AM, Saptarshi Guha w

Re: [Rd] How to set user read request while R install

2014-02-07 Thread Simon Urbanek
Sandip, this has nothing to do with R but rather your restrictive umask setting. If you want others to have rx permissions, change your umask to something like 0022 which is more commonly used (please see unix documentation on the concepts involved). Cheers, Simon On Feb 7, 2014, at 1:15 PM

Re: [Rd] Redefining .Call

2014-02-08 Thread Simon Urbanek
btw. > Ideally, you should not be using PACKAGE in the first place - it's mostly for backwards compatibility. Modern packages should be using cached symbols created by useDynLib() since they are much faster than looking up symbols for every call which unnecessary and slow. Che

Re: [Rd] $new cannot be accessed when running from Rscript and methods package is not loaded

2014-02-11 Thread Simon Urbanek
nk that has been solved, so conceptually I think this is a bug that could be fixed. This sounds like something that should be possible to fix - even if it means fixing something in R to make it happen. Working around it in hacky ways mentioned here doesn't solve the underlying prob

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