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Dear all I was thinking about efficient reading data into R and tried several ways to test if load(file.Rdata) or readRDS(file.rds) is faster. The files file.Rdata and file.rds contain the same data, the first created with save(d, ' file.Rdata', compress=F) and the second with saveRDS(d, ' file.rds', compress=F). First I used the function microbenchmark() and was a astonished

I spent a lot of time searching and came up empty handed on the following query. Is there an equivalent to rowSums that does product or cumulative product and avoids use of apply or looping? I found a rowProd in a package but it was a convenience function for apply. As part of a likelihood calculation called from optim, I?m computing products and cumulative products of rows of matrices with

Hi all, I'm working with a bunch of large graphs, and stumbled across something useful. Probably many of you know this, but I didn't and so others might benefit. Using pch="." speeds up plotting considerably over using symbols. > x <- runif(1000000) > y <- runif(1000000) > system.time(plot(x, y, pch=".")) user system elapsed 1.042 0.030 1.077

The large value for maximum time may be due to garbage collection, which happens periodically. E.g., try the following, where the unlist(as.list()) creates a lot of garbage. I get a very large time every 102 or 51 iterations and a moderately large time more often mb <- microbenchmark::microbenchmark({ x <- as.list(sin(1:5e5)); x <- unlist(x) / cos(1:5e5) ; sum(x) }, times=1000)

Dear R-ophiles, I've found something very odd when I apply convolve to ever larger vectors. Here is an example below with vectors ranging from 2^11 to 2^17. There is a funny bump up at 2^12. Then it gets very slow at 2^16. > for( i in 11:20 )print( system.time(convolve(1:2^i,1:2^i,type="o"))) user system elapsed 0.002 0.000 0.002 user system elapsed 0.373

I just finished compiling openssh-2.1.0p3 on a SCO openserver system. I generated the keys fine and genereated the host keys both rsa and dsa without problems. ssh (version1) works great. I tried to use ssh (version 2) and after being prompted to login, it quits. I am attaching a script file of... ssh -v -2 root at sco to see if you can find the problem. Let me know how I can help. [root at

Note that if you force a garbage collection each iteration the times are more stable. However, on the average it is faster to let the garbage collector decide when to leap into action. mb_gc <- microbenchmark::microbenchmark(gc(), { x <- as.list(sin(1:5e5)); x <- unlist(x) / cos(1:5e5) ; sum(x) }, times=1000, control=list(order="inorder")) with(mb_gc,

Suharto, If you're interested in performance with subscripting, you might want to look at pqR (pqR-project.org). It has some substantial performance improvements for subscripting over R Core versions. This is especially true for the current development version of pqR (probably leading to a new release in about a month). You can look at a somewhat-stable snapshot of recent pqR development

On Tue, Jul 11, 2017 at 11:39 AM, Jo Goossens <jo.goossens at hosted-power.com> wrote: > Hello Joe, > > > > > > I just did a mount like this (added the bold): > > > mount -t glusterfs -o > *attribute-timeout=600,entry-timeout=600,negative-timeout=600,fopen-keep-cache* > ,use-readdirp=no,log-level=WARNING,log-file=/var/log/glusterxxx.log >

I've looked at how to speed up the transpose function in R (ie, t(X)). The existing code does the work with loops like the following: for (i = 0; i < len; i++) REAL(r)[i] = REAL(a)[(i / ncol) + (i % ncol) * nrow]; It seems a bit optimistic to expect a compiler to produce good code from this. I've re-written these loops as follows: for (i = 0, j = 0; i<len; i +=

Hello Joe, ? ? I just did a mount like this (added the bold): ? mount -t glusterfs -o attribute-timeout=600,entry-timeout=600,negative-timeout=600,fopen-keep-cache,use-readdirp=no,log-level=WARNING,log-file=/var/log/glusterxxx.log 192.168.140.41:/www /var/www ?Results: ? root at app1:~/smallfile-master# ./smallfile_cli.py ?--top /var/www/test --host-set 192.168.140.41 --threads 8 --files 5000

Hi, I am using Van Dyke SecureCRT 3.2.1 to access an AIX server running OpenSSH-2.5.0p1. Using ssh1 with X11 forwarding enabled, the server reports the following error (in the client session): Packet integrity error. (34) This problem was not evident in 2.3.0p1. Running sshd in debug gives the output: debug1: sshd version OpenSSH_2.5.1p1 debug1: load_private_key_autodetect: type 0 RSA1

Hi, I believe I have significantly improved [dpq]wilcox functions by implementing Harding's algorithm: Harding, E.F. (1984): An Efficient, Minimal-storage Procedure for Calculating the Mann-Whitney U, Generalized U and Similar Distributions, App. Statist., 33, 1-6 Results on my computer show (against R-2.9.1): > system.time( dwilcox( 800, 800, 80) ) user system elapsed 0.240

You need to study how reading files works in your operating system. This question is not about R. -- Sent from my phone. Please excuse my brevity. On August 22, 2017 5:53:09 AM PDT, raphael.felber at agroscope.admin.ch wrote: >Dear all > >I was thinking about efficient reading data into R and tried several >ways to test if load(file.Rdata) or readRDS(file.rds) is faster. The

Hello Vijay, ? ? What do you mean exactly? What info is missing? ? PS: I already found out that for this particular test all the difference is made by :?negative-timeout=600 , when removing it, it's much much slower again. ? ? Regards Jo ? -----Original message----- From:Vijay Bellur <vbellur at redhat.com> Sent:Tue 11-07-2017 18:16 Subject:Re: [Gluster-users] Gluster native mount is

Hi Ben, here is the output from sshd -d -d -d: mvs2:sygm:/usr/local/sbin:#./sshd -d -d -d debug3: Reading output from 'ls -alni /var/log' debug3: Time elapsed: 459 msec debug2: Command 'ls -alni /var/log' timed out debug3: Got 0.00 bytes of entropy from 'ls -alni /var/log' debug3: Reading output from 'ls -alni /var/adm' debug3: Time elapsed: 143 msec debug2:

I've only recently started using R. One of the problems I come up against is after having extracted a large dataset (>5M rows) out of database, I realize I need another variable. In this case I have data frame with dates. I want to find the minimum date for each value of x1 and add that minimum date to my data.frame. > randomdf <- function(p) { data.frame(x1=sample(1:10^4, 10^p,

setTimeLimit(elapsed=1) causes a timeout error whenever a call takes more than one second. For instance, this is how it works on Windows (R 3.3.1): > setTimeLimit(elapsed=1) > Sys.sleep(10); message("done") Error in Sys.sleep(10) : reached elapsed time limit Also, the error propagates immediately and causes an interrupt after ~1 second; > system.time({ Sys.sleep(10);

I''m trying to time a function within Firefoxwith a pid$target probe [2]. e.g dtrace -Zqw -x dynvarsize=64m -x evaltime=preinit -p 13954 -s menu- construct.d -s sigcont.d elapsed: 12.7942481ms cpu : 7.7911194ms count : 40 times I''m also measuring Firefox startup time by running it arguments like this: ... file:///Users/joelr/work/mozilla/startup/startup.html#`python

Hi Ben, I test the command sshd -d -d -d several times and mostly the sshd-Daemon not started and sometimes the sshd-Daemon started, with the message: debug1: Seeded RNG with 16 bytes from programs debug1: Seeded RNG with 3 bytes from system calls debug1: sshd version OpenSSH_2.9p1 debug1: private host key: #0 type 0 RSA1 debug1: Bind to port 22 on 0.0.0.0. Server listening on 0.0.0.0 port 22.