On Thu, 18 Jul 2019, Jan Galkowski wrote:
> I have confirmed that a complete workaround to these problems is available
> if, as Bill Dunlap suggested, "version=2" is used in all *save* incantations.
That will mask this particular symptom, but the real problem is that
the C++ code in the package
My apologies
On Thu, Jul 18, 2019 at 4:00 PM Bert Gunter wrote:
> This query should almost certainly be posted on the Bioconductor Help site
> rather than here. Especially so as it is a general question about a
> genomics "workflow" rather than a question about R programming.
>
> Bert Gunter
>
>
This query should almost certainly be posted on the Bioconductor Help site
rather than here. Especially so as it is a general question about a
genomics "workflow" rather than a question about R programming.
Bert Gunter
"The trouble with having an open mind is that people keep coming along and
sti
Good evening,
I am dealing with an already analyzed .RData file consisting of
pre-configured data objects loaded into my environment. I am attempting to
take this data, which shows an overall correlation of survival with
methylation pattern for a form of brain cancer, and go to the individual
Peter, it appears to be the same as this bug:
https://github.com/xianyi/OpenBLAS/issues/2168
I added my info to the discussion.
Thanks for the reminder.
And thank you again to Ivan for the help.
Sarah
On Thu, Jul 18, 2019 at 3:17 PM Peter Langfelder
wrote:
>
> Sarah, if you haven't done so
Sarah, if you haven't done so already, please do us (OpenBLAS users) a
big favor and report the bug, either to Fedora or directly to OpenBLAS
maintainers.
Peter
On Thu, Jul 18, 2019 at 11:46 AM Sarah Goslee wrote:
>
> Wow. You are entirely correct. I would not have been able to pinpoint
> the pr
I have confirmed that a complete workaround to these problems is available if,
as Bill Dunlap suggested, "version=2" is used in all *save* incantations.
Thanks Bill!
- Jan
On Thu, Jul 18, 2019, at 10:39, William Dunlap wrote:
> Note that you can reproduce this in R-3.5.1 if you specify serial
Wow. You are entirely correct. I would not have been able to pinpoint
the problem, or how to test it. Thank you.
I am unhappy you are right, since these are the fast workstations I
use for all of my heavy-duty analysis, and it's not even *possible* to
rerun everything.
Oh dear.
Here, with the op
Thanks Jim,
I appreciate that you spend so much time helping me on this.
I translated your code to use my plot_ly function this way, I'm not sure if
this is correct, but tried to match your x and y axis and the labels. Here is
the complete code including data below, but it seems like my code "ti
On Thu, 18 Jul 2019 13:30:09 -0400
Sarah Goslee wrote:
> I'm not even remotely a hardware expert: if the difference is due to
> changes in the instruction set, I assume that has potential
> consequences for other things, and I just happened to spot it in this
> particular case because it's visual
I'll address all of your questions below, but starting with this:
> Could any of the computers
exhibiting the bizarre behaviour be equipped with an AVX-512-capable
CPU?
Yes. Both computers that are giving the bizarre results have Intel
i9-7900X CPUs; the X-series apparently is AVX-512-capable.
T
But it's also a convenience feature. Note that $E returned null
because there was an ambiguity. By the time you got to $Ex the column
you were referencing was unambiguous and you didn't have to type out
the whole thing. Useful if you have very long column names, for
example imported from a spreadsh
On Thu, 18 Jul 2019 11:50:17 -0400
Sarah Goslee wrote:
> The problem is in the conversion from RGB to Lab.
Hmm. Assuming defaults and skipping all checks, convertColor(red.rgb,
from = "sRGB", to = "Lab") amounts to the following:
red.rgb <- t(col2rgb(rep('red',8), alpha = 0)/255)
# let's hope t
I didn't include enough detail, despite the length of my original
email. The problem is in the conversion from RGB to Lab. I converted
it back to RGB because most of us are more familiar with that. Below
are the intermediate steps.
And to make it even more bizarre, it fails with eight or more colo
Hello Yannick,
That behavior is documented in the help for subsetting ( ?'$' ):
Both ‘[[’ and ‘$’ select a single element of the list. The main
difference is that ‘$’ does not allow computed indices, whereas
‘[[’ does. ‘x$name’ is equivalent to ‘x[["name", exact =
FALSE]]’.
Hello all
I noticed today that you can access dataframe columns by using incomplete
names. This is a really unexpected behavior which led to some unexpected errors
and I was wondering whether it's a bug or not and whether it should be changed
in the future.
Here's a working example using the pre
Something about the deferred string conversion object in
a <- names(attributes(apresX)[[4]][[1]][[1]])
is malformed; .Internal(inspect(a)) also infinite loops.
Will try to narrow this down.
Best,
luke
On Thu, 18 Jul 2019, William Dunlap via R-help wrote:
> If you use version=3, ascii=TRUE and
If you use version=3, ascii=TRUE and look at the file made up to the point
of the error, you can see a quasi-infinite repeat of a block of 165 numbers
(after a deferred string called "base"?). Looks like inappropriate
recursion.
Bill Dunlap
TIBCO Software
wdunlap tibco.com
On Thu, Jul 18, 2019
This is, indeed, bizzare!
On Thu, 18 Jul 2019 10:35:57 -0400
Sarah Goslee wrote:
> I've gotten as far as locating the problem in this line from
> grDevices::convertColor()
>
> xyz <- from$toXYZ(color, from.ref.white)
So if you manually feed the arguments:
Lab <- structure(c(53.48418378524
Note that you can reproduce this in R-3.5.1 if you specify serialization
version 3 (which became the default in 3.6.0).
> save(apresX, file="351-2.RData", version=2)
> save(apresX, file="351-2.RData", version=3)
Error: C stack usage 7969184 is too close to the limit
> version$version.string
[1] "
I am getting unexpected results when converting from RGB to Lab. This
is clearly some kind of configuration problem, but I cannot find it. I
have three linux workstations, both fully updated (except all are
running R 3.6.0 instead of 3.6.1, because that's the latest Fedora 30
binary). I'm running R
Hi Steven,
I caved in and installed plotly. Not an easy task. When I tried your
example, I got a blank HTML page displayed. I then created a plot with
your data above showing every third monthday label. If this is what
you want, maybe the way I have coded it will work in plotly.
sydf$date<-as.Date
> # Test for saving. Jan Galkowski, 17th July 2019.
> # produceProtectionFault.R
>
> library(apcluster)
> cl1 <- cbind(rnorm(100, 0.2, 0.05), rnorm(100, 0.8, 0.06))
> cl2 <- cbind(rnorm(50, 0.7, 0.08), rnorm(50, 0.3, 0.05))
> x <- rbind(cl1, cl2)
>
> ## compute similarity matrix and run affinity
> "JG" == Jan Galkowski
> on Tue, 16 Jul 2019 21:56:28 -0400 writes:
JG> Did something seriously change in R 3.6.1 at least for Windows in terms
of stack impacts?
JG> I'm encountering many problems with the 00UNLOCK, needing to disable
locking during installations.
JG
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