similar to: parLapply on sqlQuery (from package RODBC)

Hi, This is my first message to this list. It would be great if people here could help me with the following problem (self-contained code example below): I have a list of matrices and would like to apply a summary function to the matrices in the list. The matrices represent social networks, therefore I need to apply some specialized summary functions provided by the ergm package. These

Hi, Here are the issues I found: Typos ----- (a) Found: It a parallel version of ?evalq?, "is" missing. (b) Found: 'parLapplyLB', 'parSapplyLB' are load-balancing versions, intended for use when applying ?FUN? to 'parLapplyLB' has no 'FUN' arg (more on this below). (c) Found: 'clusterApply' calls 'fun' on the first

Hi R-developers In the package Parallel, the function parLapply(cl, x, f) seems to allow transmission of only one parameter (x) to the function f. Hence in order to compute f(x, y) parallelly, I had to define f(x, y) as f(x) and tried to access y within the function, whereas y was defined outside of f(x). Script: library(parallel) f <- function(x) { z <- 2 * x + .GlobalEnv$y # Try to

I am having the following problem with RODBC I connect to an oracle 8i (8.1.7) database using RODBC as follows; dbConn <- odbcConnect("mydatabase","myuserid","mypassword",case="oracle") Then I extract some data, actually a whole table; orgdata <- sqlQuery(dbConn, "select * from organism", na.strings = "NA") Then I try to save it

I just joined and though I did quickly read the posting guide it is quite possible not going to be a perfect posting. For one I tried to figure out how to reply to an existing message on the topic. I gave up but figured I keep at least the same subject. In a gist I get an empty data frame after issuing the following select query from R 2.9.1 to Oracle 10.2.0.1 64bit via RODBC 1.3 and Oracle 11g

invoking parLapply without a cluster fails to find a previously registered cluster > library(parallel) > setDefaultCluster(makePSOCKcluster(2)) > parLapply(X=1:2, fun=function(...) {}) Error in cut.default(i, breaks) : invalid number of intervals This is because in parLapply length(cl) is determined before defaultCluster(cl) is called. By inspection, this appears to be true of

Dear R users, I have some problems with the parLapply function from the "parallel" package: I use parLapply on a pretty big R object without changing the object within the called function. If I execute parLapply alone, everything works fine. It seems that the object resides only once in the memory. But if I use the same call within another function, the object seems to be multiplied to

The runtime of parallel::parLapply depends on variables unrelated to the parLapply call. However, this is not clearly documented. Therefore I would like to suggest expanding the relevant documentation to explain this behaviour. Consider this example: parallel_demo <- function(random_values_count) { some_data <- runif(random_values_count) dummy_function <- function(x) { x }

Dear R-user, I am trying to use the function 'parLapply' from the 'snow' package which is supposed to work the same wys as 'lapply' but for a parallelized cluster of computers. The function I am trying to call in parallel is 'dudi.pca' (from the 'ade4' package) which performs principal component analyses. When I call this function on a list of

I am slightly confused by the way the standard output is redirected in a R snow cluster environment. I am using parLapply from the snow package to execute a function on my MPI/LAM cluster. How can I redirect standard output (produced using "cat") from this function back to the terminal where I invoked it? I intend to transmit some status information in advance to the final result of the

Dear R-users I was running into problems with my R code trying to run clh sampling (clhs package) in parallel mode (=on various data sets simultaneously). Here is the code (which I developed with some help:)): ****************************************** library("clhs") library("snow") a <- as.data.frame(replicate(1000, rnorm(20))) b <- as.data.frame(replicate(1000,

Hello everybody, I've got a bit of a problem with parLapply that's left me scratching my head today. I've tried this in R 2.11 and the 23 bit Revolution R Enterprise and gotten the same result, OS in question is Windows XP, the package involved is the snow package. I've got a list of 20 rain/no rain (1/0) situations for these two stations i and j, all the items in this list look

Hi, The following function use to work, but now it doesn't giving the error "> CallSnow(, 100) Using snow package, asking for 2 nodes 2 slaves are spawned successfully. 0 failed. Error in checkForRemoteErrors(val) : 2 nodes produced errors; first error: no applicable method for 'lapply' applied to an object of class "list" ". Where this is the

Dear R gurus, I have a very embarrassingly parallelizable job that I am trying to speed up with snow on our local cluster. Basically, I am doing ~50,000 t.test for a series of micro-array experiments, one gene at a time. Thus, I can easily spread the load across multiple processors and nodes. So, I have a master list object that tells me what rows to pick up for each genes to do the t.test from

Dear All, Is the following expected behaviour? set.seed(1) library(parallel) cl = makeCluster(5) clusterSetRNGStream(cl, iseed = NULL) parSapply(cl, 1:5, function(i) sample(1:10, 1)) # 7 4 2 10 10 clusterSetRNGStream(cl, iseed = NULL) # 7 4 2 10 10 parSapply(cl, 1:5, function(i) sample(1:10, 1)) stopCluster(cl) The documentation could be read either way, e.g. * iseed: An integer to be

I'm parallelizing some computation on hierarchical data, and would find it natural to do something like this (where a call to parLapply is embedded in outer call to parLapply): cl <- makeCluster(rep.int('localhost', 5), type='SOCK') clusterExport(cl, 'cl') parLapply(cl, 1:5, function(i) parLapply(cl, 1:5, function(j) i * j)) Snow

Dear All, I want to connnect R with oracle. I am using RODBC package for this connection. Following is my code to connect library(RODBC) channel <- odbcConnect("Vikrant") I am getting following error. 1: In odbcDriverConnect("DSN=Vikrant") : [RODBC] ERROR: state NA000, code 12288, message [Microsoft][ODBC driver for Oracle][Oracle]ORA-12514: TNS:listener does not

Hi everyone, I'm aiming to run an external executable (say filetorun.EXE) in parallel. The external executable collect needed data from a file, say "input.txt" and, in turn,generates several output files, say "output.txt". I need to generate "input.txt", run the executable and keep "input.txt" and "output.txt". I'm using Windows 7, R

Hi, I'm trying to use RODBC without having to set up a DSN, using hte direct connection string in odbcDriverConnect. My connection attempt looks something like: > odbcDriverConnect(connection = "SERVER=localhost;DRIVER={/usr/lib/odbc/libmyodbc.so};DATABASE=myDB;UID=reader;PASSWORD=insecure;") And this returns the message: Warning messages: 1: In odbcDriverConnect(connection =

I am sure I'm doing something wrong here but not sure what. Our system administrator recently installed UnixODBC and the MyODBC driver on a Linux box running Linux version 2.6 x86_64. I have an .odbc.ini file in my home directory with following lines: [mydb] Description = MySQL server on my-server Driver=/usr/lib64/libmyodbc3.so SERVER=my-server I can successfully do the following: