On Fri, Nov 9, 2012 at 3:05 PM, gianluca mastrantonio
gianluca.mastranto...@yahoo.it 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
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
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
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
On Tue, Aug 20, 2013 at 9:23 AM, peter dalgaard pda...@gmail.com 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
000 0 0
It looks like there is an issue with larger matrices when calling diag
function and it has nothing to do with WGCNA.
On 8/20/13 9:43 AM, Peter Langfelder peter.langfel...@gmail.com wrote:
Hi Sam,
I assume you mean that correlation for _genes_ (not samples)
11262
On Tue, Aug 20, 2013 at 11:41 AM, ivo welch ivo.we...@anderson.ucla.edu 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
On Fri, Sep 27, 2013 at 2:50 PM, Kasper Daniel Hansen
kasperdanielhan...@gmail.com 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
On Tue, Oct 15, 2013 at 1:15 PM, Paul Johnson pauljoh...@gmail.com 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
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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R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
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:
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
murdoch.dun...@gmail.com wrote:
On 20/08/2014, 4:11 PM, Peter Langfelder wrote:
The default format= in as.Date.character
On Wed, Aug 20, 2014 at 4:52 PM, Gabriel Becker gmbec...@ucdavis.edu 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
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
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
peter.langfel...@gmail.com wrote:
Hi all,
just installed the current version of R-devel (2015-01-13 r67453) from
CRAN. Package checking via CMD check
Thanks!
Peter
On Thu, Aug 6, 2015 at 12:07 PM, Dirk Eddelbuettel e...@debian.org 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 least) R
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
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
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
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
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
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
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
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
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
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
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
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)])
to read
the GenomicFeatures vignette.
Best,
Jim
On Tue, Jan 13, 2015 at 12:34 AM, Peter Langfelder
peter.langfel...@gmail.com wrote:
Hi all,
can anyone please explain or point me to an explanation of how to
replace org.Hs.egCHR and friends that appear to be deprecated in the
devel
Hi all,
can anyone please explain or point me to an explanation of how to
replace org.Hs.egCHR and friends that appear to be deprecated in the
devel version? The deprecation message isn't very helpful. Thanks!
x = org.Hs.egCHR
Warning message:
In (function () :
org.Hs.egCHR is deprecated.
Hi Bernat,
my advice may not be that useful, but it may be better than the
silence so far...
Regarding the ordering of objects in hclust, if you're willing to do a
bit of hacking, have a look at the stats::hclust function; you will
see that the ordering is computed by a call to Fortran function
FWIW, the link does work for me.
Peter
On Mon, Jan 27, 2020 at 10:55 AM Shepherd, Lori <
lori.sheph...@roswellpark.org> wrote:
> That is unfortunate - We have checked the link and it does seem accurate
> and works for our network and out of network collaborators.
>
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