similar to: gdistance::shortestPath throws error "not a symmetric matrix"

I mistakenly left a write in "/tmp" in the rockchalk package (version 1.8.109) that I uploaded last Friday. Kurt H wrote and asked me to fix today. While uploading a new one, I became aware of a problem I had not seen. The version I uploaded last Friday, 1.8.109, has OK status on all platforms except r-release-windows-ix86+x86_64. I get OK on oldrel-windows and also on devel-windows.

1. Martin Maechler's comments should be taken as replacements for anything I wrote where appropriate. Any apparent conflict is a result of his superior knowledge. 2. 'eigen' returns the eigenvalue decomposition assuming the matrix is symmetric, ignoring anything in m[upper.tri(m)]. 3. The basic idea behind both posdefify and nearPD is to compute the

>>>>> Paul Johnson <pauljohn32 at gmail.com> >>>>> on Mon, 20 Nov 2017 14:59:26 -0600 writes: > I mistakenly left a write in "/tmp" in the rockchalk package (version > 1.8.109) that I uploaded last Friday. Kurt H wrote and asked me to fix > today. > While uploading a new one, I became aware of a problem I had not seen.

Hi, I am running R 3.3.3 and getting the following error: Error in add_edges(res, edges = t(as.matrix(el[, 1:2])), attr = weight) : long vectors not supported yet: ../../src/include/Rinlinedfuns.h:138 when passing a 13 GB TransitionLayer object to shortestPath from the package 'gdistance'. The error, albeit in a different context, is discussed here:

This looks to me like a package development issue... which may be under discussion in R-sig-geo (search the archives), but more likely to be appropriate to discuss with the maintainer by email or through their development repository (R-forge, though it looks unused). -- Sent from my phone. Please excuse my brevity. On February 14, 2018 7:43:51 AM PST, Loris Bennett <loris.bennett at

Hi Jeff, Jeff Newmiller <jdnewmil at dcn.davis.ca.us> writes: >> Hi, >> >> I am running R 3.3.3 and getting the following error: >> >> Error in add_edges(res, edges = t(as.matrix(el[, 1:2])), attr = weight) >> : >> long vectors not supported yet: ../../src/include/Rinlinedfuns.h:138 >> >> when passing a 13 GB TransitionLayer

Hard to follow data analysis without data. Try making your example reproducible [1][2][3] and post in plain text (a setting in your emailer). Read the Posting Guide mentioned in the footer to avoid other posting pitfalls. [1] http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example [2] http://adv-r.had.co.nz/Reproducibility.html [3]

hello, I have a graph and i use qgraph package to calculate centrality parameters. Now I want to know the maximum value of shortest path for each vertex with discarding the Inf value in short pathes. For this I use the ShortestPathLengths of centrality function in qgraph. but when I want to get the maximum the result is wrong. here is my code: cen<-centrality(Q)

HI, I am really messing up to make a symmetrical matrix using upper.tri() & lower.tri() function. Here is my code:   > set.seed(1) > mat = matrix(rnorm(25), 5, 5) > mat            [,1]       [,2]       [,3]        [,4]        [,5] [1,] -0.6264538 -0.8204684  1.5117812 -0.04493361  0.91897737 [2,]  0.1836433  0.4874291  0.3898432 -0.01619026  0.78213630 [3,] -0.8356286  0.7383247

Dear R Users, I am having trouble with lmer. I am looking at recombinant versus non recombinant individuals. In the response variable recombinant individuals are coded as 1's and non-recombinant as 0's. I built a model with 2 fixed factors and 1 random effect. Sex (males/females) is the first fixed effect and sexual genotype (XY, YY, WX and WY) the second one. Sexual Genotype is

A new version of "the Matrix" (well, actually the R package named "Matrix") has become available on the CRAN mirrors. As some of you have noticed, the version numbers (current is version 0.999375-8) are converging to one, and we feel that we have solved enough of the many (mostly small) problems to announce that release 1.0-0 is imminent. In the DESCRIPTION of the package

A new version of "the Matrix" (well, actually the R package named "Matrix") has become available on the CRAN mirrors. As some of you have noticed, the version numbers (current is version 0.999375-8) are converging to one, and we feel that we have solved enough of the many (mostly small) problems to announce that release 1.0-0 is imminent. In the DESCRIPTION of the package

Dear all, My code is presented as the following. library(MASS) library(rmutil) library(repeated) library(lme4) library(arm) #install.packages("Zelig", repos = "http://gking.harvard.edu") library(Zelig) rm(list = ls()) beta0<-2.5 beta1<--0.3 sigs2<-0.5 I<-4 #numberpatients<-c(40,100,160,200,400,600) numberpatients<-c(1000) #numberpatients<-3 times<-1

Sorry if this answer was already given, or if I miss the point, but did you have a look to "lowerTriangle" and "upperTriangle" functions in the "gdata" package ? # example # A<-matrix(rnorm(9),3,3) # B<-B<-matrix(NA,dim(A)[1],dim(A)[2]) # lowerTriangle(B)<-lowerTriangle(A) # upperTriangle(B)<-lowerTriangle(A) # diag(B)<-diag(A) Hope this helps,

Using Igraph, I create shortest paths, then convert the matrix into three column vectors - "vertex1", "vertex2", "shortestpath" - as the code below shows. #code for generating shortest path matrix and creating a 3 columns from an igraph graph object "y" y_s<-shortest.paths(y, weights = NULL) y_s <- melt(y_s)[melt(upper.tri(y_s))$value,] #Step 2: this

Hi, We've observed rather strange behavior related to as(). When as() is used to make a conversion to a super class, an invalid entry is inserted into the table of methods. > setClass("A", contains="list") > get(".MTable", environment(coerce))[["list#A"]] NULL > as(list(), "A") > get(".MTable",

Dear R list members I would be grateful if anyone could guide me to a solution for fixing my rimage package problem described below. I recently upgraded my machine from fedora core 3 to fedora core 6 and then upgraded R from version 2.3.1 from version 2.4.1. I then fired up R, tried to load the rimage library and received the following messages: > library(rimage) Error in dyn.load(x,

Hi (again), let's say I want to create a class Matrix that extends the class matrix, but I can't get it to work. I define the class as > setClass("Matrix", "matrix") > getClass("Matrix") No Slots, prototype of class "matrix" Extends: Class "matrix" directly. Class "structure" by class "matrix".

Hi: I was trying to use apply on a sparse matrix from package Matrix, and I get the error: Error in asMethod(object) : Cholmod error 'problem too large' at file ../Core/cholmod_dense.c, line 106 Is there a way to apply a function to all the rows without bumping into this problem? Here is a simplified example: > dim(sm) [1] 72913 43052 > class(sm) [1] "dgCMatrix"

Hello, <http://tolstoy.newcastle.edu.au/R/help/04/07/0312.html#0313qlink1> Could anybody tell me how to generate discrete Laplacian distribution? I need to sample uma discretised Laplacian density like this: J( g -> g´) ~ exp (-lambda | g´ - g |) g in {0,…, gmax} Thanks, Nicolette [[alternative HTML version deleted]]