similar to: Bug in gplots::heatmap.2 symbreaks arg default (?)

Hi all, Sometimes I'll find myself "ctrl-c"-ing like a madman to kill some code that's parallelized via foreach/doMC when I realized that I just set my cpu off to do something boneheaded, and it will keep doing that thing for a while. In these situations, since I interrupted its normal execution, foreach/doMC doesn't "clean up" after itself by killing the

Hi Yan, Before I try to answer your question: please send R questions to the r- help mailing list (cc'd here). You will likely get your answer more quickly (since I'm not the only one looking at it) and it might help other people who get stuck on a similar situation by finding the answer on a public forum (just like you did). On Sep 8, 2009, at 5:44 AM, Yan Hui wrote: > Dear

Hi Sadaf, Out of curiosity, what sorts of things have you tried to fix this? For example, after playing around with this a bit, if I remove your "eps" parameter from your `ranges` list, it works. Perhaps you should try tweaking the values you pick for your parameters. You don't even have to put it in the `tune` function to get an idea of the ranges you should use: R>

Hi all, Trying to do what my subject says. As I'm trying to be better about making packages out of my code, I'd like the packages themselves to be better, which means *.Rd- documenting my code. The thing is, from years of programming other languages prior to landing in the R pond, I've grown accustomed to documenting my functions inline. I'm not just used to it, but I like

Hi, I was wondering if there was a way to store the results of a computationally expensive "getter" call on an S4 object, so that it is only calculated once for each object. Trivial example: let's say I want to cache the "expensive" area calculation of a square object. setClass("Square", representation( length='numeric',

Hi all, This feature was throwing me for a loop for quite some time until I played with the names of the slots. Consider exhibit A: ============== setClass("SVM", representation=representation( x='numeric', y='numeric', C='numeric', eps='numeric'), prototype=prototype( x=numeric(),

Hi Abbas, Before I try to give you answers, I just want to mention that you should send R related reqests to the R-help list, and not me personally because (i) there's a greater likelihood that it will get answered in a timely manner, and (ii) people who might have a similar problem down the road might benefit from any answer via searching the list archives ... anyway: On Sep 5, 2009, at

I have written a wrapper for heatmap.2 called heatmap.w.row.and.col.clust which auto-generates breaks using breaks<-round((c(seq(from=(-20 * stddev), to=(20 * stddev))))/20, digits = 2) #(stddev in this case = 2.5) This has always worked well in the past but now I am getting an error that non-finite breaks are being generated. Drilling down, it seems that my wrapper is generating finite

Hi Jeannine, I'm just forwarding this Q&A back to the r-help list, you'll get more eyes on it and other people might have better solutions. Answers inline: On Sep 11, 2009, at 12:25 PM, Jeannine Cavender-Bares wrote: > Dear Steve, > > Greetings! You helped me earlier this summer with an R question in > response to a message Brian McCarthy put out on the listserv. I

Hi, Essentially: subject line says it all. I've created a package that wraps an external c++ library (which I didn't write) that only successfully compiles on 64bit machines. I'd like to make the package broadly available, but is there a way to get it on CRAN if the 32-bit builds break by specifying its 64-bit only somehow? Luckily, I've ./configure'd my

Hi, [I sent this to the plyr mailing list (late) last night, but it seems to be lost in the moderation queue, so here's a shot to the broadeR community] Apologies in advance for being more verbose than necessary, but I'm not even sure how to ask this question in the context of plyr, so ... here goes. As meaningless as this might be to do with the `iris` data, the spirit of it is what

Hi all, In short: I'm running ddply on an admittedly (somehow) large data.frame (not that large). It runs fine until it finishes and gets to the "collating" part where all subsets of my data.frame have been summarized and they are being reassembled into the final summary data.frame (sorry, don't know the correct plyr terminology). During collation, my R workspace RAM usage goes

In pvec(list(1, 2), FUN, mc.cores=2) FUN sees integer() arguments whereas pvec(list(1, 2, 3), FUN, mc.cores=2) FUN sees list() arguments; the latter seems consistent with pvec's description. This came up in a complicated Bioconductor thread about generics and parallel evaluation https://stat.ethz.ch/pipermail/bioc-devel/2012-October/003745.html One relevant point is that a

Hi all, I'm putting together some common code + data into a custom package, everything is working out fine, but the ``R CMD INSTALL MyPackage`` call seems to take a particularly long time in the "**data" step: $ R CMD INSTALL MyPackage/ * installing to library ?/Library/Frameworks/R.framework/Resources/ library? * installing *source* package ? MyPackage? ... ** R ** data

Hi Claire, I'm replying and CC-ing to the R-help list to get more eyes on your question since others will likely have more/better advice, and perhaps someone else in the future will have a similar question, and might find this thread handy. I've removed your specific research aim since that might be private information, but you can include that later if others find it necessary to know

Dear All, Thank you kindly for such detailed replies. I was looking to overlay data using algorithms so that i am able to tell which genes are differentially expressed due to changes in copy number. I did a pubmed search and found only 7 literature pieces all of which use in-house algorithms. I am yet to explore Gviz since it wouldn't work on R 2.14, would try it after upgrading to R 2.15.

I got the data working, but now I got another problem with KSVM: line search fails -2.793708 -0.5831701 1.870406e-05 -5.728611e-06 -5.059796e-08 -3.761822e-08 -7.308871e-13Error in prob.model(object)[[p]]$A : $ operator is invalid for atomic vectors On Tue, Jul 7, 2009 at 6:45 PM, Steve Lianoglou<mailinglist.honeypot at gmail.com> wrote: > Hi, > > On Jul 7, 2009, at 6:44 PM,

Hi I am trying to understand what happen with the heatmap.2 code that it used to work (last used in October 2015). I am able to get a heatmap but my colour key doesn't come up and instead I get an error in all my files the used to work. Does anyone has any idea of what could have changed? or how to fix this. Thanks. # Error in seq.default(min.raw, max.raw, by = min(diff(breaks)/100)) :

Hi, I'm using R-2.12 on a linux 64bit machine. When I run a chunk of code inside a foreach() %do% { ...} or %dopar% {...} (with doMC backend) I keep getting a segfault. Running the *same* code within lapply(something, function(x) ... ) doesn't result in any segfaults. I'll paste the output below, but I'm not sure it would be helpful. I'm more curious how to go about smoking

Hi, I was wondering if I could get R to warn me, or give me a rude awakening somehow, if I'm accessing a variable that is out of my function's scope. For example, often times I'm creating a function as I'm testing it in the REPL, copying and pasting between both. As a simple example, I might end up with a function like: f <- function(a, b) { a + b.test } Where