Hi all,
apologies if I missed something here. Just downloaded and compiled
R-patched from https://stat.ethz.ch/R/daily/ but it reports as R-4.3.3
(2024-04-09 r86895) -- "Angel Food Cake". The last dated R-patched is
from 2024-04-09, about 3 months old. Are R-patched not updated
anymore, am I looki
On Sat, May 11, 2024 at 9:34 AM luke-tierney--- via R-devel
wrote:
>
> On Sat, 11 May 2024, Travers Ching wrote:
>
> > The following code snippet causes R to hang. This example might be a
> > bit contrived as I was experimenting and trying to understand
> > promises, but uses only base R.
>
> This
Hi all,
this may have been noticed/discussed before but my search came up
empty, so here it is: hist.default throws a (somewhat cryptic) error
when trying to call it on a long vector. The error is
invalid length(x)
and is thrown because lines 4 and 5 or so are
n <- length(x <- x[is.finite(x)])
I'm also not a native speaker but my take is that a "be" is missing in
the sentence and it should read
An expression, which if it evaluates to TRUE the debugger will be invoked,
otherwise control is returned directly.
On Wed, Jul 28, 2021 at 11:52 PM Rui Barradas wrote:
>
> Hello,
>
> R 4.1.0 on
I think your character vector got converted to a factor. See ?options,
section stringsAsFactors:
‘stringsAsFactors’: The default setting for arguments of
‘data.frame’ and ‘read.table’.
The default is TRUE, so strings get converted to factors when building
data frames.
Set options(s
Unless this is something Apple-specific, the problem seems to be with
Gimp, not with R. On my system (linux), opening your examples with
either firefox or inkscape shows huge letters. At least firefox should
be able to open the svg on a Mac as well. BTW, Gimp on linux does not
open your cex-svg.svg
On Sat, Jun 1, 2019 at 3:22 AM Therneau, Terry M., Ph.D. via R-devel
wrote:
>
> In the next version of the survival package I intend to make a non-upwardly
> compatable
> change to the survfit object. With over 600 dependent packages this is not
> something to
> take lightly, and I am currently
On Wed, May 8, 2019 at 9:00 AM Ralf Stubner wrote:
> AFAIK a single-threaded OpenBLAS is used. When compiling R from source
> on a CentOS system I have used the configure option
> '--with-blas="-lopenblasp"' to link with the pthread version of OpenBLAS.
Yes, that's the right incantation. Thanks
F, cairo
>
> Options not enabled: memory profiling
>
>
> Recommended packages:no
>
>
>
> so it doesn't look like it's using the openBlas... how come the arguments
> to ./configure are being ignored?
>
>
>
>
> hankin.ro...@gmail.com
I'm a linux guy so take the advice with a grain of salt... When you
run the configure script, look at the output at the end of the run, it
should either say
Options enabled: shared BLAS, ... (means you are using R BLAS)
or it should mention OpenBLAS in External libraries (meaning you
Does this help a little?
https://cran.r-project.org/doc/manuals/r-release/R-ints.html#Long-vectors
One thing I seem to remember but cannot find a reference for is that
long vectors can only be passed to .Call calls, not C/Fortran. I
remember rewriting .C() in my WGCNA package to .Call for this ve
Some time ago I (and some other CRAN package maintainers) got an email
from Brian Ripley (copied below) regarding compiler warnings under gcc
8.1. In my case this concerns package PropClust
(https://CRAN.R-project.org/package=PropClust). The check with gcc 8.1
(https://www.stats.ox.ac.uk/pub/bdr/gc
On Tue, Feb 13, 2018 at 2:20 AM, Jeroen Ooms wrote:
> Thanks for your question. Your logs show that 'gcc' is not found. As
> of R 3.3 you need to set the path to the compiler using the BINPREF
> variable. This is because we ship two separate versions of gcc, one
> targeting win32 and one targetin
Hi all,
I'm trying to set up the Windows Rtools toolset for building packages
with compiled code. I installed for Windows R-3.4.3 from CRAN and
installed Rtools-3.4 in a custom location M:\R\R-3.4.3 and
M:\R\Rtools-3.4
Following the instructions, in shell, I set
Path=M:\R\Rtools-3.4\bin;M:\R\Rtoo
I would be very cautious about OpenBLAS in particular... from time to
time I get complains from users that compiled code calculations in my
WGCNA package crash or produce wrong answers with large data, and they
all come from OpenBLAS users. I am yet to reproduce any of their
crashes when using MKL
FWIW, I tried it on my linux box. The memory use shot through the roof, the
system crawled to a halt due to constant swapping, and after a minute or so
top showed memory use of 47GB, at which point I killed the R process. On
linux at least R is not frozen but the strsplit call gobbles up memory (an
Thanks!
Peter
On Thu, Aug 6, 2015 at 12:07 PM, Dirk Eddelbuettel wrote:
>
> On 6 August 2015 at 11:33, Peter Langfelder wrote:
> | Just downloaded the newest R-patched.tar.bz. DEcompressing and
> | untarring now produces a directory R-beta instead of the usual (for
> | me, at lea
Just downloaded the newest R-patched.tar.bz. DEcompressing and
untarring now produces a directory R-beta instead of the usual (for
me, at least) R. The file VERSION now says 3.2.2 beta. Just wanted to
double-check that there is no mixup of development and patched
versions.
Thanks,
Peter
Apologies... missed Michal's email and the discussion of the same topic.
Thanks,
Peter
On Wed, Jan 14, 2015 at 6:15 PM, Peter Langfelder
wrote:
> Hi all,
>
> just installed the current version of R-devel (2015-01-13 r67453) from
> CRAN. Package checking via CMD check suddenl
Hi all,
just installed the current version of R-devel (2015-01-13 r67453) from
CRAN. Package checking via CMD check suddenly prints a lot of notes
that complain of ... used in a situation where it does not exist. A
prototypical example is
fa = function(...)
{
fb(...)
}
where fa and fb are defi
On Wed, Aug 20, 2014 at 4:52 PM, Gabriel Becker wrote:
> Could do both to preserve bc...
>
> if(missing(format) || !nchar(format))
>
No, the problem is that the function behaves differently when format
is missing than when it equals its default. Removing this difference
necessarily changes behavi
That would be my preferred solution, but it would break backwards
compatibility for format="", so others may disagree.
Peter
On Wed, Aug 20, 2014 at 1:18 PM, Duncan Murdoch
wrote:
> On 20/08/2014, 4:11 PM, Peter Langfelder wrote:
>> The default format="" in a
The default format="" in as.Date.character is supremely confusing. The
help shows as.Date defined as
## S3 method for class 'character'
as.Date(x, format = "", ...)
yet the function behaves very differently when format is not specified
and when it is specified to its default:
as.Date("2012-
Hello,
would it be possible to install the Bioconductor package impute on the
machine that checks and builds binary packages for OSX 10.9 Mavericks?
Thanks,
Peter
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On Tue, Oct 15, 2013 at 1:15 PM, Paul Johnson wrote:
> Dear R Devel
>
> Some of our R users are still insisting we run R-2.15.3 because of
> difficulties with a package called OpenMX. It can't cooperate with new R,
> oh well.
>
> Other users need to run R-3.0.1. I'm looking for the most direct ro
On Fri, Sep 27, 2013 at 2:50 PM, Kasper Daniel Hansen
wrote:
> Peter,
>
> This is a relatively "new" warning from R CMD check (for some definition of
> new). The authors of Hmisc have clearly not yet gone through the process of
> cleaning it up, as you are doing right now (and there are many othe
Hi all,
one of my packages uses the rcorr.cens function from the Hmisc
package. Until now I have simply put the Hmisc package into Depends:,
but prodded on by new CRAN requirements, I tried to moving it into
Imports:. However, this fails because rcorr.cens calls the function
is.Surv from survival,
On Tue, Aug 20, 2013 at 11:41 AM, ivo welch wrote:
> I am using a variant of stopifnot a lot. can I suggest that base R
> extends its functionality? I know how to do this for myself. this is
> a suggestion for beginners and students. I don't think it would break
> anything.
>
> first, I think
0 0 0
> [3,]000000000 0 0
> [4,] 00 0000000 0 0
> [5,]000000000 0 0
> [6,]000000000 0 0
> [7,]0
On Tue, Aug 20, 2013 at 9:23 AM, peter dalgaard wrote:
> What is bicor()? From the WGCNA package? Perhaps the package is doing
> something incompatible with the long vector support in R 3.0.0. You need to
> report such queries to the maintainer.
The maintainer is reporting for duty :)
The ver
Hi Sam,
I assume you mean that correlation for _genes_ (not samples)
11262:3 is 0? I am the maintainer of the WGCNA package but
unfortunately I don't have access to a Mac big enough to try
3x3 correlation matrix, but I would be thankful if you could
try reproducing the problem with sma
Hi all,
it appears that plot.hclust disregards the argument 'cex'. Up until
2.15.1 (and probably all 2.15.x), specifying cex in plot.hclust
changed the size of the plotted labels on each leaf. In 3.0.0 the
character size remains the same irrespective of the cex setting. Since
the help text for plo
Hi all,
I maintain the WGCNA package which at present has nearly 200
functions. In the future there will be more. Curious whether it would
be preferable or useful to split the package into a couple different
ones with different aims. Obviously, when one calls a function in R,
package name spaces h
On Fri, Nov 9, 2012 at 3:05 PM, gianluca mastrantonio
wrote:
> the error "memory non mapped" happen also if i use
> void FiltroGaus(SEXP size1_r, SEXP size2_r, SEXP sigma_r)
> instead
> SEXP FiltroGaus(SEXP size1_r, SEXP size2_r, SEXP sigma_r) {
>
If you use a .Call on a function, the function mu
I'm not an expert, but from what I know you should certainly use the
.Call interface when you define a function as you did. The problem is
that your function must return a value (of type SEXP) which it does
not. If you don't return a value, all bets are off as to what will
happen, and if the intern
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