Frameworks/R.Framework/Versions/2.3/Resources/
> library"
>
The default on OS X is
> .libPaths()
[1] "/Library/Frameworks/R.framework/Resources/library"
>
in the shell and
> .libPaths()
[1] "/Library/Frameworks/R.framework/Versions/2.3/Resources/library&
Hi List,
I am trying to come to terms with embedding R. I have looked in
writing R extensions and a pdf slideshow (by Simon Urbanek) I found on
the web and by my reckoning the following should almost work (I use
function Rf_initEmbeddedR in the file winembed.c from the Rserv source
to initialise
or me. As Peter
mentioned earlier my guess is that you failed to use/define the
correct encoding.
Cheers,
Simon
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t; I'm not sure about the wording of the user prompt
> Duncan> question, which is now "Quit and discard
> Duncan> workspace?". The problem with this wording is that
> Duncan> someone who automatically hits "y" will lose their
> Dunc
reason you stated I think that's a major problem!
>> The correct approach is to change the default button, but
>> definitely not the dialog box.
>
> I don't think this is sufficient.
>
Your solution may possibly be more efficient in solving the problem
you
On Jul 4, 2006, at 4:26 AM, [EMAIL PROTECTED] wrote:
> This seems to crash my version of R: "
>
Thanks. Now fixed in the GUI rev. 3283.
There's still an open issue about the completion of empty names, but
I need to dig more to solve that (at least it doesn't cras
fault that it doesn't work ...
.. and since you pounding on OO - environments are the closest you
can get to an object semantics as implemented in the most popular OO
languages, so I wonder why you aren't arguing to make all objects
into references ;).
Cheers,
Simon
_
u. Apparently something segfaults in your
script, so you should attach a debugger to the process that is
segfaulting and see what exactly crashes.
Cheers,
Simon
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On Jul 5, 2006, at 2:23 PM, Gabor Grothendieck wrote:
> On 7/5/06, Simon Urbanek <[EMAIL PROTECTED]> wrote:
>
> I don't think ad hominem arguments and unsupported statements that
> things "make no sense" or analogies to screwdrivers have any
> relevance to
R,
>
JRI is a low-level interface, so may need to learn more about R.
However, the experimental JRI 0.3 is getting some higher-level API
and is available from http://www.rosuda.org/R/nightly/
Cheers,
Simon
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On Jul 7, 2006, at 2:05 PM, Vincent Yau wrote:
> Simon:
>
> Would JRI able to also invoke stuff from R packages that I have
> installed?
> (e.g Bioconductor)
>
Of course. JRI starts the same R as the RGUI or R console. R is run
as one thread in your Java application
://r.research.att.com/ is compiled with gcc 4.0.3 and it doesn't
exhibit this behavior.
Cheers,
Simon
On Jul 11, 2006, at 5:04 AM, Robin Hankin wrote:
> Hi Martin
>
>
> On 11 Jul 2006, at 09:25, Martin Maechler wrote:
>
>> I assume this is specific to your installation of R-d
and that was it!
>
> Oh btw Simon, I couldn't find the run.bat in the JRI_0.2-4.tar.gz
> file. I found a "run.in" but that is a unix bash script.
>
run (and run.bat respectively) are created by make, so you should run
"sh configure.win; make" on Windows or
tory is empty on Bioc, because none of the packages compiles).
I have now also committed the fix (thanks to Seth for the correct
analysis and fix).
Cheers,
Simon
> -Original Message-
> From: Herve Pages [mailto:[EMAIL PROTECTED]
> Sent: Tue 7/18/2006 12:51 PM
> To: Stev
s that
implements RMainLoopCallbacks and simple reng.eval("print(a)"); will
cause rWriteConsole to be called with the output. This approach is
more suitable for console-like GUIs.
Cheers,
Simon
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ur Applications folder - there is no installer.
If you use the regular CRAN installer of a released version of R
(2.3.1) then the GUI is installed as a part of the R installation
process, so it has no separate check. I have also checked the
individual package (which usually is not used directly) an
ike
.First.lib <- function(libname, pkgname) {
library.dynam("myPackage", pkgname, libname)
}
in your package (or use useDynLib if your package has a namespace).
If it still doesn't help, try it without the PACKAGE=.. argument and
load the .so manually using dyn.load
y machine with curl) a way to upload a file
successfully is
curl --disable-epsv -T MYPACKAGE ftp://cran.R-project.org/incoming/
Note that CRAN doesn't work if you use EPSV (which many ftp programs
do by default).
Cheers,
Simon
[[alternative HTML v
known to contain bugs that were fixed since (even at that
point the CRAN page was recommending an update). Please use R 2.3.1 +
most recent GUI and tell us whether you can still reproduce the bug.
Thanks,
Simon
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h
even tell us what package you are talking about.
Cheers,
Simon
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s index for repository
> http://cran.fhcrc.org/bin/macosx/x86_64/contrib/2.3
^^ we don't build binaries for x86_64 architecture, so you cannot use
that (Apple didn't release Leopard yet, so there is no 64-bit Intel
binaries around a
in libRlapack. It is
now fixed in the current R-devel.
The current R-devel now also checks the Xcode capabilities and will
fall-back to flat namespaces if the linker is too old (the other
error reported here). I tested some combinations of BLAS and tools,
but not all of them, so pleas
On Aug 8, 2006, at 2:52 AM, Prof Brian Ripley wrote:
> On Mon, 7 Aug 2006, Simon Urbanek wrote:
>
>> Herve,
>>
>> On Aug 7, 2006, at 11:34 AM, [EMAIL PROTECTED] wrote:
>>
>>> Recently I needed to download a few R packages for Unix, Windows
>>> and
padding out to a multiple of 8 bytes.
>
Although it's not a bug in R, it is a problem with the Mac binary
which uses static libjpeg. I have re-compiled libjpeg for Intel Mac
so tonight's nightly build should be ok.
Thanks,
Simon
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padding out to a multiple of 8 bytes.
>
Although it's not a bug in R, it is a problem with the Mac binary
which uses static libjpeg. I have re-compiled libjpeg for Intel Mac
so tonight's nightly build should be ok.
Thanks,
Simon
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a bug - please see the FAQ for Mac OS X - you cannot mix
compiler versions. Use either gcc3+g77 or gcc4+gfortran.
Cheers,
Simon
> After running gnu make (version 3.8) I get the following error:
>
> Error in dyn.load(x, as.logical(local), as.logical(now)) :
> unable to load
3 results (ran with R
2.4.0) - there is pretty much no difference between the binaries
except for the 37x37 test and the explanation is above.
Cheers,
Simon
I. Matrix calculation gcc3 gcc4d CRAN
-
Creation, transp., deformation
ze me first!
> x
Error: you have to initialize me first!
> failed<-FALSE
> x
[1] "I'm foo"
Is there a way to achieve that? Intuitively I'd think that this is
the desired behavior, because currently the promise is sort of
'broken' after an error (AFA
;, d(),assign.env=ae)})
However in my particular case the whole point of using a promise is
that I'm dealing with a sealed environment (namespace) so you cannot
re-install delayedAssign again (it will fail because the binding is
locked). If the promise worked as I envision, re-installing
ter the VM was
initialized - using them before is an error). I have an ugly work-
around for that as well, the question was whether promises could be
used for that purpose as a more clean solution and the answer appears
to be no - at least for R <=2.4.
Seth,
thanks for the suggestions.
On Oct 18, 2006, at 11:23 AM, Seth Falcon wrote:
> Simon Urbanek <[EMAIL PROTECTED]> writes:
>> thanks, but this is not what I want (the symbols in the environment
>> are invisible outside) and it has nothing to do with the question I
>
omise code. This is basically poor man's version of 3)
Personally I would vote for 3), but I can see the arguments for 1).
Cheers,
Simon
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r than 99.
You may want to increase the margin size in the preferences if you
wish to see the full number.
Although not a bug per se, it could be useful to align the line
numbers on the right instead.
Cheers,
Simon
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R-devel@r-project.org mailin
oo limited to be really of significant
use in R and real threaded R is not on the horizon anytime soon.
However, approaches like snow were suitable for most parallelization
tasks I have encountered in R... So unless someone writes a lot of
[the right] code (which would be great!) it's unl
specified at configure time. Depending on your cctools, you may
not be able to use the new system, so possibly you have to use ./
configure --with-blas='-framework vecLib' --with-lapack
Cheers,
Simon
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Jon,
I don't have access to a Mac Pro, so I can't test anything, but based
on your report I found a bug in R_system that affects signal handling
during "system" calls on Macs. Please test the current R-devel
(39754) or R-2-4-branch (39755) to see if it solves your pro
later when it can't find ".jnew", as you'd expect.
> But there's no spurious syntax error.)
>
> Because of the difficulties with the debugger I'm going to quit
> now; if you find any evidence that suggests it really is R's bug
> after all,
ylib.o yields an error message:
> /usr/bin/libtool: unknown option character `m' in: -macosx_version_min
>
Please update your Xcode - the libtool is too old.
Cheers,
Simon
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cross versions -
i.e. you can set R_LIBS such that you have version-specific directory
first and a common directory second.
> (I see that R CMD INSTALL has a "--with-package-versions" option,
> but I think that's about using mult
machine or not.
Cheers,
Simon
On Nov 30, 2006, at 7:43 PM, stefano iacus wrote:
> Jeff,
> this is not a bug report for R, and you already posted to R-Sig-mac
> (and get answered)
> Maybe you want to contact the author of MagicMenu (or what ever is
> the software you use) to understand
be way more that the time spent in the parser. Actually I'm wondering
whether you checked it at all, because I'd almost certainly expect
the evaluation to take way more time than the parsing step. If it
does, I'd be inclined to think
IX_C_SOURCE has the side-effect of enabling __DARWIN_UNIX03 on OS
X, so _APPLE_C_SOURCE is an alternative if we want to restrict this
to OS X only (it has the same effect, though).
Cheers,
Simon
> OSes who adopt pretty standard function names with non-standard
> implementations used
Thanks, Seth,
it's now fixed in R-devel.
Cheers,
Simon
On Jan 8, 2007, at 10:54 AM, Seth Falcon wrote:
> Hi,
>
> A recent change has R failing to compile (for me) on ppc OSX 10.4.8
> like this:
>
> ../../../../R-devel/src/main/datetime.c: In function `reset_tz'
(process.getErrorStream()), buffSize);
Regards Simon
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Java 1.6 on 64-bit
systems (fine being defined by the fact that JGR works :)). JGC-based
JRE is still quite buggy on both 32 and 64-bit machines as far as we
can tell, but for non-GUI task it seems to work. However, I don't
think this is what Brian has in mind ...
Cheers,
Simon
ng, whether this API
> change was intentional or not.
Yes, it was intentional (added support for keep.source I believe).
Duncan, you may want to add the API change to NEWS - it's not
mentioned there.
Cheers,
Simon
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e one supplied by wine. The hhw path in MkRules must
then point to the local directory on the host (because it's used for
the headers files) and you'll have to create shell-wrapper for hhc
that looks somewhat like "wine hhc.exe $*".
Cheers,
Simon
>
>> On Fri, 19
to use C++ then RInside is a nice package that wraps the R
API in C++ classes for easier use: https://github.com/eddelbuettel/rinside
simplifying it quite a bit.
Cheers,
Simon
PS: this list is for the discussions on *development* of R itself, please
consider using the R-help mailing list
Jirko,
> On Dec 9, 2024, at 8:57 AM, Jiří Moravec wrote:
>
> Dear Simon and Jeroen,
>
> thank you for your answers. I have to reiterate that I am out of my depth in
> here. My knowledge of http is clicking links and not much beyond that.
>
> I will definitely
nt to use it for.
There may be use-cases which do fit the design so we could make it happen. I
would recommend looking at Rserve first, because anything implemented there is
trivial to add to R (as it is the same code base) if it would make sense. So
I'm open to suggestions, but they
toolchain and all library versions as well.
Cheers,
Simon
> On Feb 10, 2025, at 10:08 PM, Tobias Verbeke
> wrote:
>
> L.S.
>
> AFAICS the Writing R Extensions and R Installation and Administration manuals
> do not explicitly discuss binary R packages on GNU/Linux. Only inst
it can use the CRAN binaries), so it requires cooperation across the
spectrum including the distros. That said, the Linux maintainers are certainly
invited to liaise with CRAN if they think it would be beneficial to host things
on CRAN - we have done in the past, but with the explosion of dist
VISUAL - it's just a default when neither
the system nor user doesn't declare their preference. I don't think R should be
fishing for random programs that may or may not be editors at run-time.
Cheers,
Simon
> On Dec 11, 2024, at 5:08 AM, Michael Chirico
> wrote:
>
>
27;ll find code like
if (++i % 1 == 0) R_CheckUserInterrupt(); in loops to make sure it's not
called unnecessarily.
Cheers,
Simon
> On Dec 18, 2024, at 4:04 AM, Ben Bolker wrote:
>
> This seems like a great idea. Would it help to escalate this to a post on
> R-bugzilla
(and breaking things) would have any benefit.
Typically, the only use-case for full 64-bit integers is as opaque 64-bit
storage (e.g., randomly generated IDs) but there arithmetics make no sense
there and packages are already covering that need.
Cheers,
Simon
> On Jan 25, 2025, at 11:08 PM, Ton
Please see the GSoC schedule - for 2025 the organisation applications won't
close until February 12 so we may not know the answer until possibly sometime
in March (that's assuming there are proposed projects).
Cheers,
Simon
> On Jan 22, 2025, at 6:23 AM, Greg Forkutza wrote:
. I was thinking of using xz as that is more stable, already
supported and less controversial, but I don’t think the choice really matters -
it just has to be a compression which R supports (zstd and xz have different
benefits, so it’s always a trade-off without a clear winner).
Cheers,
Simon
oerce integers to doubles. Technically the latter would be more
consistent with R, but if someone explicitly passes an integer to the inverse
logit function in a real application then chances are it’s not intentional.
Cheers,
Simon
> Fixed in R-devel,
>
> Best,
> Tomas
>
>
Heather,
thanks, now fixed (datasets was using numeric value for compress= instead of
the compression name so it picked zstd instead of gzip - now the switch order
is kept the same).
Cheers,
Simon
> On Jan 15, 2025, at 10:21 PM, Heather Turner wrote:
>
> With the changes to
Dandan,
thanks! Dirk reported it as
https://bugs.r-project.org/show_bug.cgi?id=18884
and it should be fixed in R-devel r88154 - please confirm if it works for you
and if it does, I'll port it to R 4.5.0 Patched.
Cheers,
Simon
> On Apr 17, 2025, at 3:40 PM, zhangdandan wrote:
>
uages.
>
Why not? They all require compilers, ways to deal with dependencies and produce
binaries - so does Rust. It's just one of many similar languages. The key is to
have proper support instead of having each package deal with the complexities
alone.
Cheers,
Simon
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ndency sources etc.) are to be addressed, as
opposed to making random demands. All this has nothing to do with CRAN so the
issue you mention seems irrelevant to the progress. Also I'd like to know what
are the "challenges embedded in R itself".
Cheers,
Simon
> On Mar 2, 2
ck, so, yes, agreed.
Without valid use-cases I'm not convinced yet that an override is a good idea
since it may get out of sync just as you noted, but I may be just missing a
valid use-case. That said, if the override is paired with the check, i.e., if
both your proposals are implemen
below a simple somewhat reproducible (usually it
crashes around 5.5GB of vsize, sometimes it gets into an infinite
loop) exemple and the relevant sessionInfo.
Is this a "normal" limitation of R, a problem with my config or a
*cough* bug ?
best regards,
Simon.
> l<-list(1
cific, I guess I'll see if I can
get some help from Simon Urbanek and his mac know-how...
> This example will allocate large generic vectors and then allocate
> lots of copies of 1 to fill it in. Can you reproduce the problem with
> something of coarser granularity, e.g. pasting toge
onnection(g, open = "r") :
the 'wininet' method of url() is deprecated for http:// and https:// URLs
So I get a warning, but it works.
I guess this boils down to two questions:
1. Is it possible to add the same "method" argument to gzfi
tion was unable
to check revocation for the certificate.
Error in
download.file("https://seurat.nygenome.org/azimuth/references/homologs.rds";, :
'curl' call had nonzero exit status
I realise that this may not be as simple as the certificate not being seen, and
that t
В Thu, 12 Sep 2024 15:06:50 +
Simon Andrews пишет:
> > > download.file('https://seurat.nygenome.org/azimuth/references/homolo
> > > gs.rds', destfile = "c:/Users/andrewss/homologs.rds", method="curl")
<...>
> > cu
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